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commit/galaxy-central: clem...@galaxyproject.org: Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.*
by Bitbucket 02 Nov '12

02 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c0f9edeb7ab1/ changeset: c0f9edeb7ab1 user: clem...(a)galaxyproject.org date: 2012-10-31 23:41:13 summary: Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.* affected #: 27 files diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/index.rst --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -3,22 +3,19 @@ Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. - - Accessible: Users without programming experience can easily specify - parameters and run tools and workflows. - - Reproducible: Galaxy captures information so that any user can repeat and - understand a complete computational analysis. - - Transparent: Users share and publish analyses via the web and create - Pages, interactive, web-based documents that describe a complete - analysis. + +- Accessible: Users without programming experience can easily specify parameters and run tools and workflows. +- Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis. +- Transparent: Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis. Contents ======== .. toctree:: - :maxdepth: 4 + :maxdepth: 5 - API Documentation <lib/galaxy.web.api> + API Documentation <lib/galaxy.webapps.galaxy.api> - Application Documentation <lib/galaxy> + Application Documentation <lib/modules> Indices and tables ================== diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.datatypes.converters.rst --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -113,6 +113,14 @@ :undoc-members: :show-inheritance: +:mod:`interval_to_fli` Module +----------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_fli + :members: + :undoc-members: + :show-inheritance: + :mod:`interval_to_interval_index_converter` Module -------------------------------------------------- diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.deferred.rst --- a/doc/source/lib/galaxy.jobs.deferred.rst +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -17,6 +17,14 @@ :undoc-members: :show-inheritance: +:mod:`genome_index` Module +-------------------------- + +.. automodule:: galaxy.jobs.deferred.genome_index + :members: + :undoc-members: + :show-inheritance: + :mod:`genome_transfer` Module ----------------------------- diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.rst --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -25,6 +25,14 @@ :undoc-members: :show-inheritance: +:mod:`mapper` Module +-------------------- + +.. automodule:: galaxy.jobs.mapper + :members: + :undoc-members: + :show-inheritance: + :mod:`transfer_manager` Module ------------------------------ @@ -40,6 +48,7 @@ galaxy.jobs.actions galaxy.jobs.deferred + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.cli_job.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.cli_job.rst @@ -0,0 +1,19 @@ +cli_job Package +=============== + +:mod:`cli_job` Package +---------------------- + +.. automodule:: galaxy.jobs.runners.cli_job + :members: + :undoc-members: + :show-inheritance: + +:mod:`torque` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.cli_job.torque + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.cli_shell.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.cli_shell.rst @@ -0,0 +1,19 @@ +cli_shell Package +================= + +:mod:`cli_shell` Package +------------------------ + +.. automodule:: galaxy.jobs.runners.cli_shell + :members: + :undoc-members: + :show-inheritance: + +:mod:`rsh` Module +----------------- + +.. automodule:: galaxy.jobs.runners.cli_shell.rsh + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.rst --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -9,6 +9,22 @@ :undoc-members: :show-inheritance: +:mod:`cli` Module +----------------- + +.. automodule:: galaxy.jobs.runners.cli + :members: + :undoc-members: + :show-inheritance: + +:mod:`condor` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.condor + :members: + :undoc-members: + :show-inheritance: + :mod:`drmaa` Module ------------------- @@ -57,3 +73,11 @@ :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.runners.cli_job + galaxy.jobs.runners.cli_shell + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.backports.importlib.rst --- /dev/null +++ b/doc/source/lib/galaxy.util.backports.importlib.rst @@ -0,0 +1,11 @@ +importlib Package +================= + +:mod:`importlib` Package +------------------------ + +.. automodule:: galaxy.util.backports.importlib + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.backports.rst --- /dev/null +++ b/doc/source/lib/galaxy.util.backports.rst @@ -0,0 +1,18 @@ +backports Package +================= + +:mod:`backports` Package +------------------------ + +.. automodule:: galaxy.util.backports + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.util.backports.importlib + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.rst --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -137,3 +137,10 @@ :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.util.backports + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -0,0 +1,43 @@ +phyloviz Package +================ + +:mod:`phyloviz` Package +----------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz + :members: + :undoc-members: + :show-inheritance: + +:mod:`baseparser` Module +------------------------ + +.. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`newickparser` Module +-------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`nexusparser` Module +------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`phyloxmlparser` Module +---------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.data_providers.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -0,0 +1,42 @@ +data_providers Package +====================== + +:mod:`data_providers` Package +----------------------------- + +.. automodule:: galaxy.visualization.data_providers + :members: + :undoc-members: + :show-inheritance: + +:mod:`basic` Module +------------------- + +.. automodule:: galaxy.visualization.data_providers.basic + :members: + :undoc-members: + :show-inheritance: + +:mod:`genome` Module +-------------------- + +.. automodule:: galaxy.visualization.data_providers.genome + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: galaxy.visualization.data_providers.registry + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.visualization.data_providers.phyloviz + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.genome.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -0,0 +1,19 @@ +genome Package +============== + +:mod:`genome` Package +--------------------- + +.. automodule:: galaxy.visualization.genome + :members: + :undoc-members: + :show-inheritance: + +:mod:`visual_analytics` Module +------------------------------ + +.. automodule:: galaxy.visualization.genome.visual_analytics + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.rst --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -22,5 +22,7 @@ .. toctree:: + galaxy.visualization.data_providers + galaxy.visualization.genome galaxy.visualization.tracks diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.tracks.rst --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -9,14 +9,6 @@ :undoc-members: :show-inheritance: -:mod:`data_providers` Module ----------------------------- - -.. automodule:: galaxy.visualization.tracks.data_providers - :members: - :undoc-members: - :show-inheritance: - :mod:`summary` Module --------------------- @@ -25,11 +17,3 @@ :undoc-members: :show-inheritance: -:mod:`visual_analytics` Module ------------------------------- - -.. automodule:: galaxy.visualization.tracks.visual_analytics - :members: - :undoc-members: - :show-inheritance: - diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.api.rst --- a/doc/source/lib/galaxy.web.api.rst +++ /dev/null @@ -1,352 +0,0 @@ -Galaxy API Documentation -************************ - -Background -========== -In addition to being accessible through a web interface, Galaxy can now also be -accessed programmatically, through shell scripts and other programs. The web -interface is appropriate for things like exploratory analysis, visualization, -construction of workflows, and rerunning workflows on new datasets. - -The web interface is less suitable for things like - - Connecting a Galaxy instance directly to your sequencer and running - workflows whenever data is ready - - Running a workflow against multiple datasets (which can be done with the - web interface, but is tedious) - - When the analysis involves complex control, such as looping and - branching. - -The Galaxy API addresses these and other situations by exposing Galaxy -internals through an additional interface, known as an Application Programming -Interface, or API. - -Quickstart -========== - -Set the following option in universe_wsgi.ini and start the server:: - - enable_api = True - -Log in as your user, navigate to the API Keys page in the User menu, and -generate a new API key. Make a note of the API key, and then pull up a -terminal. Now we'll use the display.py script in your galaxy/scripts/api -directory for a short example:: - - % ./display.py my_key http://localhost:4096/api/histories - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc - name: Unnamed history - id: 8c49be448cfe29bc - #2: /api/histories/33b43b4e7093c91f - name: output test - id: 33b43b4e7093c91f - -The result is a Collection of the histories of the user specified by the API -key (you). To look at the details of a particular history, say #1 above, do -the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc - Member Information - ------------------ - state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} - state: ok - contents_url: /api/histories/8c49be448cfe29bc/contents - id: 8c49be448cfe29bc - name: Unnamed history - -This gives detailed information about the specific member in question, in this -case the History. To view history contents, do the following:: - - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - name: Pasted Entry - type: file - id: 6f91353f3eb0fa4a - -What we have here is another Collection of items containing all of the datasets -in this particular history. Finally, to view details of a particular dataset -in this collection, execute the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0f… - Member Information - ------------------ - misc_blurb: 1 line - name: Pasted Entry - data_type: txt - deleted: False - file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat - state: ok - download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt - visible: True - genome_build: ? - model_class: HistoryDatasetAssociation - file_size: 17 - metadata_data_lines: 1 - id: 6f91353f3eb0fa4a - misc_info: uploaded txt file - metadata_dbkey: ? - -And now you've successfully used the API to request and select a history, -browse the contents of that history, and then look at detailed information -about a particular dataset. - -For a more comprehensive Data Library example, set the following option in your -universe_wsgi.ini as well, and restart galaxy again:: - - admin_users = you(a)example.org - library_import_dir = /path/to/some/directory - -In the directory you specified for 'library_import_dir', create some -subdirectories, and put (or symlink) files to import into Galaxy into those -subdirectories. - -In Galaxy, create an account that matches the address you put in 'admin_users', -then browse to that user's preferences and generate a new API Key. Copy the -key to your clipboard and then use these scripts:: - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - - 0 elements in collection - - % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' - Response - -------- - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 - Member Information - ------------------ - synopsis: None - contents_url: /api/libraries/f3f73e481f432006/contents - description: API Test Library - name: api_test - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - - % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' - Response - -------- - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: api_test_folder1 - id: 28202595c0d2591fa4f9089d2303fd89 - - % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 - Response - -------- - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: 2.bed - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: 3.bed - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: /api_test_folder1 - type: folder - id: 28202595c0d2591fa4f9089d2303fd89 - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: /api_test_folder1/2.bed - type: file - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: /api_test_folder1/3.bed - type: file - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87… - Member Information - ------------------ - misc_blurb: 68 regions - metadata_endCol: 3 - data_type: bed - metadata_columns: 6 - metadata_nameCol: 4 - uploaded_by: nate@... - metadata_strandCol: 6 - name: 2.bed - genome_build: hg19 - metadata_comment_lines: None - metadata_startCol: 2 - metadata_chromCol: 1 - file_size: 4272 - metadata_data_lines: 68 - message: - metadata_dbkey: hg19 - misc_info: uploaded bed file - date_uploaded: 2010-06-22T17:01:51.266119 - metadata_column_types: str, int, int, str, int, str - -Other parameters are valid when uploading, they are the same parameters as are -used in the web form, like 'link_data_only' and etc. - -The request and response format should be considered alpha and are subject to change. - - -API Controllers -=============== - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.web.api.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.web.api.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.web.api.genomes - :members: - :undoc-members: - :show-inheritance: - -:mod:`histories` Module ------------------------ - -.. automodule:: galaxy.web.api.histories - :members: - :undoc-members: - :show-inheritance: - -:mod:`history_contents` Module ------------------------------- - -.. automodule:: galaxy.web.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`libraries` Module ------------------------ - -.. automodule:: galaxy.web.api.libraries - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_contents` Module ------------------------------- - -.. automodule:: galaxy.web.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`permissions` Module -------------------------- - -.. automodule:: galaxy.web.api.permissions - :members: - :undoc-members: - :show-inheritance: - -:mod:`quotas` Module --------------------- - -.. automodule:: galaxy.web.api.quotas - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_types` Module ---------------------------- - -.. automodule:: galaxy.web.api.request_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.web.api.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`roles` Module -------------------- - -.. automodule:: galaxy.web.api.roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`samples` Module ---------------------- - -.. automodule:: galaxy.web.api.samples - :members: - :undoc-members: - :show-inheritance: - -:mod:`tools` Module -------------------- - -.. automodule:: galaxy.web.api.tools - :members: - :undoc-members: - :show-inheritance: - -:mod:`users` Module -------------------- - -.. automodule:: galaxy.web.api.users - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualizations` Module ----------------------------- - -.. automodule:: galaxy.web.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflows` Module ------------------------ - -.. automodule:: galaxy.web.api.workflows - :members: - :undoc-members: - :show-inheritance: - - diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.base.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.base.controllers.rst @@ -0,0 +1,11 @@ +controllers Package +=================== + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.web.base.controllers.admin + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.base.rst --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -9,3 +9,10 @@ :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.web.base.controllers + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.controllers.rst --- a/doc/source/lib/galaxy.web.controllers.rst +++ /dev/null @@ -1,235 +0,0 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- - -.. automodule:: galaxy.web.controllers - :members: - :undoc-members: - :show-inheritance: - -:mod:`admin` Module -------------------- - -.. automodule:: galaxy.web.controllers.admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`admin_toolshed` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.admin_toolshed - :members: - :undoc-members: - :show-inheritance: - -:mod:`async` Module -------------------- - -.. automodule:: galaxy.web.controllers.async - :members: - :undoc-members: - :show-inheritance: - -:mod:`cloud` Module -------------------- - -.. automodule:: galaxy.web.controllers.cloud - :members: - :undoc-members: - :show-inheritance: - -:mod:`data_admin` Module ------------------------- - -.. automodule:: galaxy.web.controllers.data_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`dataset` Module ---------------------- - -.. automodule:: galaxy.web.controllers.dataset - :members: - :undoc-members: - :show-inheritance: - -:mod:`error` Module -------------------- - -.. automodule:: galaxy.web.controllers.error - :members: - :undoc-members: - :show-inheritance: - -:mod:`external_service` Module ------------------------------- - -.. automodule:: galaxy.web.controllers.external_service - :members: - :undoc-members: - :show-inheritance: - -:mod:`external_services` Module -------------------------------- - -.. automodule:: galaxy.web.controllers.external_services - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.web.controllers.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`history` Module ---------------------- - -.. automodule:: galaxy.web.controllers.history - :members: - :undoc-members: - :show-inheritance: - -:mod:`library` Module ---------------------- - -.. automodule:: galaxy.web.controllers.library - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_admin` Module ---------------------------- - -.. automodule:: galaxy.web.controllers.library_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_common` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.library_common - :members: - :undoc-members: - :show-inheritance: - -:mod:`mobile` Module --------------------- - -.. automodule:: galaxy.web.controllers.mobile - :members: - :undoc-members: - :show-inheritance: - -:mod:`page` Module ------------------- - -.. automodule:: galaxy.web.controllers.page - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_type` Module --------------------------- - -.. automodule:: galaxy.web.controllers.request_type - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.web.controllers.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests_admin` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.requests_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests_common` Module ------------------------------ - -.. automodule:: galaxy.web.controllers.requests_common - :members: - :undoc-members: - :show-inheritance: - -:mod:`root` Module ------------------- - -.. automodule:: galaxy.web.controllers.root - :members: - :undoc-members: - :show-inheritance: - -:mod:`tag` Module ------------------ - -.. automodule:: galaxy.web.controllers.tag - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_runner` Module -------------------------- - -.. automodule:: galaxy.web.controllers.tool_runner - :members: - :undoc-members: - :show-inheritance: - -:mod:`tracks` Module --------------------- - -.. automodule:: galaxy.web.controllers.tracks - :members: - :undoc-members: - :show-inheritance: - -:mod:`ucsc_proxy` Module ------------------------- - -.. automodule:: galaxy.web.controllers.ucsc_proxy - :members: - :undoc-members: - :show-inheritance: - -:mod:`user` Module ------------------- - -.. automodule:: galaxy.web.controllers.user - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualization` Module ---------------------------- - -.. automodule:: galaxy.web.controllers.visualization - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflow` Module ----------------------- - -.. automodule:: galaxy.web.controllers.workflow - :members: - :undoc-members: - :show-inheritance: - diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.rst --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -38,9 +38,7 @@ .. toctree:: - galaxy.web.api galaxy.web.base - galaxy.web.controllers galaxy.web.framework galaxy.web.security diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.community.controllers.rst --- a/doc/source/lib/galaxy.webapps.community.controllers.rst +++ b/doc/source/lib/galaxy.webapps.community.controllers.rst @@ -41,6 +41,14 @@ :undoc-members: :show-inheritance: +:mod:`repository_review` Module +------------------------------- + +.. automodule:: galaxy.webapps.community.controllers.repository_review + :members: + :undoc-members: + :show-inheritance: + :mod:`upload` Module -------------------- @@ -49,6 +57,14 @@ :undoc-members: :show-inheritance: +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.community.controllers.user + :members: + :undoc-members: + :show-inheritance: + :mod:`workflow` Module ---------------------- diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.community.framework.middleware.rst --- a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst @@ -17,3 +17,11 @@ :undoc-members: :show-inheritance: +:mod:`remoteuser` Module +------------------------ + +.. automodule:: galaxy.webapps.community.framework.middleware.remoteuser + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.api.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -0,0 +1,391 @@ +Galaxy API Documentation +************************ + +Background +========== +In addition to being accessible through a web interface, Galaxy can now also be +accessed programmatically, through shell scripts and other programs. The web +interface is appropriate for things like exploratory analysis, visualization, +construction of workflows, and rerunning workflows on new datasets. + +The web interface is less suitable for things like + - Connecting a Galaxy instance directly to your sequencer and running + workflows whenever data is ready + - Running a workflow against multiple datasets (which can be done with the + web interface, but is tedious) + - When the analysis involves complex control, such as looping and + branching. + +The Galaxy API addresses these and other situations by exposing Galaxy +internals through an additional interface, known as an Application Programming +Interface, or API. + +Quickstart +========== + +Set the following option in universe_wsgi.ini and start the server:: + + enable_api = True + +Log in as your user, navigate to the API Keys page in the User menu, and +generate a new API key. Make a note of the API key, and then pull up a +terminal. Now we'll use the display.py script in your galaxy/scripts/api +directory for a short example:: + + % ./display.py my_key http://localhost:4096/api/histories + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc + name: Unnamed history + id: 8c49be448cfe29bc + #2: /api/histories/33b43b4e7093c91f + name: output test + id: 33b43b4e7093c91f + +The result is a Collection of the histories of the user specified by the API +key (you). To look at the details of a particular history, say #1 above, do +the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc + Member Information + ------------------ + state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} + state: ok + contents_url: /api/histories/8c49be448cfe29bc/contents + id: 8c49be448cfe29bc + name: Unnamed history + +This gives detailed information about the specific member in question, in this +case the History. To view history contents, do the following:: + + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + name: Pasted Entry + type: file + id: 6f91353f3eb0fa4a + +What we have here is another Collection of items containing all of the datasets +in this particular history. Finally, to view details of a particular dataset +in this collection, execute the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0f… + Member Information + ------------------ + misc_blurb: 1 line + name: Pasted Entry + data_type: txt + deleted: False + file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat + state: ok + download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt + visible: True + genome_build: ? + model_class: HistoryDatasetAssociation + file_size: 17 + metadata_data_lines: 1 + id: 6f91353f3eb0fa4a + misc_info: uploaded txt file + metadata_dbkey: ? + +And now you've successfully used the API to request and select a history, +browse the contents of that history, and then look at detailed information +about a particular dataset. + +For a more comprehensive Data Library example, set the following option in your +universe_wsgi.ini as well, and restart galaxy again:: + + admin_users = you(a)example.org + library_import_dir = /path/to/some/directory + +In the directory you specified for 'library_import_dir', create some +subdirectories, and put (or symlink) files to import into Galaxy into those +subdirectories. + +In Galaxy, create an account that matches the address you put in 'admin_users', +then browse to that user's preferences and generate a new API Key. Copy the +key to your clipboard and then use these scripts:: + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + + 0 elements in collection + + % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' + Response + -------- + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 + Member Information + ------------------ + synopsis: None + contents_url: /api/libraries/f3f73e481f432006/contents + description: API Test Library + name: api_test + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + + % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' + Response + -------- + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: api_test_folder1 + id: 28202595c0d2591fa4f9089d2303fd89 + + % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 + Response + -------- + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: 2.bed + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: 3.bed + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: /api_test_folder1 + type: folder + id: 28202595c0d2591fa4f9089d2303fd89 + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: /api_test_folder1/2.bed + type: file + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: /api_test_folder1/3.bed + type: file + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87… + Member Information + ------------------ + misc_blurb: 68 regions + metadata_endCol: 3 + data_type: bed + metadata_columns: 6 + metadata_nameCol: 4 + uploaded_by: nate@... + metadata_strandCol: 6 + name: 2.bed + genome_build: hg19 + metadata_comment_lines: None + metadata_startCol: 2 + metadata_chromCol: 1 + file_size: 4272 + metadata_data_lines: 68 + message: + metadata_dbkey: hg19 + misc_info: uploaded bed file + date_uploaded: 2010-06-22T17:01:51.266119 + metadata_column_types: str, int, int, str, int, str + +Other parameters are valid when uploading, they are the same parameters as are +used in the web form, like 'link_data_only' and etc. + +The request and response format should be considered alpha and are subject to change. + + +API Controllers +=============== + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`folder_contents` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`folders` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_roles` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_users` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + :members: + :undoc-members: + :show-inheritance: + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups + :members: + :undoc-members: + :show-inheritance: + +:mod:`histories` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`libraries` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`permissions` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.permissions + :members: + :undoc-members: + :show-inheritance: + +:mod:`quotas` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.quotas + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`roles` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`samples` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + :members: + :undoc-members: + :show-inheritance: + +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.api.rst~ --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst~ @@ -0,0 +1,179 @@ +api Package +=========== + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`folder_contents` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`folders` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_roles` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_users` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + :members: + :undoc-members: + :show-inheritance: + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups + :members: + :undoc-members: + :show-inheritance: + +:mod:`histories` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`libraries` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`permissions` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.permissions + :members: + :undoc-members: + :show-inheritance: + +:mod:`quotas` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.quotas + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`roles` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`samples` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + :members: + :undoc-members: + :show-inheritance: + +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -0,0 +1,227 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin_toolshed` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed + :members: + :undoc-members: + :show-inheritance: + +:mod:`async` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.async + :members: + :undoc-members: + :show-inheritance: + +:mod:`cloudlaunch` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_admin` Module +------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.data_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`dataset` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.dataset + :members: + :undoc-members: + :show-inheritance: + +:mod:`error` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.error + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_service` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.external_service + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_services` Module +------------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.external_services + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`history` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.history + :members: + :undoc-members: + :show-inheritance: + +:mod:`library` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_admin` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_common` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`mobile` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.mobile + :members: + :undoc-members: + :show-inheritance: + +:mod:`page` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.page + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_type` Module +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.request_type + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_admin` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_common` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`root` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.root + :members: + :undoc-members: + :show-inheritance: + +:mod:`tag` Module +----------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.tag + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_runner` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.tool_runner + :members: + :undoc-members: + :show-inheritance: + +:mod:`ucsc_proxy` Module +------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy + :members: + :undoc-members: + :show-inheritance: + +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.user + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualization` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.visualization + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflow` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.workflow + :members: + :undoc-members: + :show-inheritance: + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -0,0 +1,19 @@ +galaxy Package +============== + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.buildapp + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.galaxy.api + galaxy.webapps.galaxy.controllers + diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.rst --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -16,5 +16,6 @@ galaxy.webapps.community galaxy.webapps.demo_sequencer + galaxy.webapps.galaxy galaxy.webapps.reports Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Circster: (a) create mixin for drawing tick labels and (b) use ticks for denoting chromosome length and track min/max.
by Bitbucket 02 Nov '12

02 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/86f05ee5dedb/ changeset: 86f05ee5dedb user: jgoecks date: 2012-11-02 21:15:15 summary: Circster: (a) create mixin for drawing tick labels and (b) use ticks for denoting chromosome length and track min/max. affected #: 1 file diff -r 154cda53407f8360ab00b54ec563c1985157c9a5 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,5 +1,9 @@ define(["libs/underscore", "libs/d3", "viz/visualization"], function(_, d3, visualization) { +/** + * Utility class for working with SVG. + */ +// TODO: make into a mixin. var SVGUtils = Backbone.Model.extend({ /** @@ -21,8 +25,89 @@ } return true; } +}); -}); +/** + * Mixin for using ticks. + */ +var UsesTicks = { + drawTicks: function(parent_elt, data, dataHandler, textTransform, horizontal) { + // Set up group elements for chroms and for each tick. + var ticks = parent_elt.append("g") + .selectAll("g") + .data(data) + .enter().append("g") + .selectAll("g") + .data(dataHandler) + .enter().append("g") + .attr("transform", function(d) { + return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + + "translate(" + d.radius + ",0)"; + }); + + // Add line + text for ticks. + var tick_coords = [], + text_coords = [], + text_anchor = function(d) { + return d.angle > Math.PI ? "end" : null; + }; + if (horizontal) { + tick_coords = [0, 0, 0, -4]; + text_coords = [4, 0, "", ".35em"]; + text_anchor = null; + } + else { + tick_coords = [1, 0, 4, 0]; + text_coords = [0, 4, ".35em", ""]; + + } + + ticks.append("line") + .attr("x1", tick_coords[0]) + .attr("y1", tick_coords[1]) + .attr("x2", tick_coords[2]) + .attr("y1", tick_coords[3]) + .style("stroke", "#000"); + + ticks.append("text") + .attr("x", text_coords[0]) + .attr("y", text_coords[1]) + .attr("dx", text_coords[2]) + .attr("dy", text_coords[3]) + .attr("text-anchor", text_anchor) + .attr("transform", textTransform) + .text(function(d) { return d.label; }); + }, + + /** + * Format number for display at a tick. + */ + formatNum: function(num, sigDigits) { + var rval = null; + if (num < 1) { + rval = num.toPrecision(sigDigits); + } + else { + // Use round to turn string from toPrecision() back into a number. + var roundedNum = Math.round(num.toPrecision(sigDigits)); + + // Use abbreviations. + if (num < 1000) { + rval = roundedNum; + } + else if (num < 1000000) { + // Use K. + rval = Math.round((roundedNum/1000).toPrecision(3)).toFixed(0) + 'K'; + } + else if (num < 1000000000) { + // Use M. + rval = Math.round((roundedNum/1000000).toPrecision(3)).toFixed(0) + 'M'; + } + } + + return rval; + } +}; /** * A label track. @@ -39,7 +124,7 @@ this.total_gap = options.total_gap; this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; - this.track_gap = 5; + this.track_gap = 10; this.label_arc_height = 50; this.scale = 1; this.circular_views = null; @@ -340,11 +425,19 @@ $.when(data_ready_deferred).then(function() { $.when(self._render_data(track_parent_elt)).then(function() { chroms_paths.style("fill", self.bg_fill); + + // Render labels after data is available so that data attributes are available. + self.render_labels(); }); }); }, /** + * Render track labels. + */ + render_labels: function() {}, + + /** * Update radius bounds. */ update_radius_bounds: function(radius_bounds) { @@ -580,52 +673,31 @@ var k = (d.endAngle - d.startAngle) / d.value, ticks = d3.range(0, d.value, 25000000).map(function(v, i) { return { + radius: self.innerRadius, angle: v * k + d.startAngle, - label: i === 0 ? 0 : (i % 3 ? null : v / 1000000 + "M") + label: i === 0 ? 0 : (i % 3 ? null : self.formatNum(v)) }; }); // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled. if (ticks.length < 4) { - ticks[ticks.length-1].label = Math.round( - ( ticks[ticks.length-1].angle - d.startAngle ) / k / 1000000 - ) + "M"; + ticks[ticks.length-1].label = self.formatNum( + Math.round( ( ticks[ticks.length-1].angle - d.startAngle ) / k ) + ); } return ticks; }; - var ticks = this.parent_elt.append("g") - .selectAll("g") - .data(this.chroms_layout) - .enter().append("g") - .selectAll("g") - .data(chromArcTicks) - .enter().append("g") - .attr("transform", function(d) { - return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + - "translate(" + self.innerRadius + ",0)"; - }); + /** Rotate and move text as needed. */ + var textTransform = function(d) { + return d.angle > Math.PI ? "rotate(180)translate(-16)" : null; + }; - ticks.append("line") - .attr("x1", 1) - .attr("y1", 0) - .attr("x2", 4) - .attr("y2", 0) - .style("stroke", "#000"); - - ticks.append("text") - .attr("x", 4) - .attr("dy", ".35em") - .attr("text-anchor", function(d) { - return d.angle > Math.PI ? "end" : null; - }) - .attr("transform", function(d) { - return d.angle > Math.PI ? "rotate(180)translate(-16)" : null; - }) - .text(function(d) { return d.label; }); + this.drawTicks(this.parent_elt, this.chroms_layout, chromArcTicks, textTransform); } }); +_.extend(CircsterChromLabelTrackView.prototype, UsesTicks); /** * View for quantitative track in Circster. @@ -683,6 +755,39 @@ .angle(line.angle()); }, + render_labels: function() { + // -- Render min and max using ticks. -- + var self = this, + // Keep counter of visible chroms. + visibleChroms = 0, + dataBoundsTicks = function(d) { + // Do not add ticks to small chroms. + if (d.endAngle - d.startAngle < 0.08) { return []; } + + // Only show bounds on every 3rd chromosome; also update visibleChroms count. + if (visibleChroms++ % 3 !== 0) { return []; } + + // Set up data to display min, max ticks. + return [ + { + radius: self.radius_bounds[0], + angle: d.startAngle, + label: self.formatNum(self.data_bounds[0]) + }, + { + radius: self.radius_bounds[1], + angle: d.startAngle, + label: self.formatNum(self.data_bounds[1]) + } + ]; + }, + textTransform = function() { + return "rotate(90)"; + }; + + this.drawTicks(this.parent_elt, this.chroms_layout, dataBoundsTicks, textTransform, true); + }, + /** * Returns an array with two values denoting the minimum and maximum * values for the track. @@ -690,6 +795,8 @@ get_data_bounds: function(data) {} }); +_.extend(CircsterQuantitativeTrackView.prototype, UsesTicks); + /** * Layout for summary tree data in a circster visualization. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: smcmanus: Temporarily reverted library browsing.
by Bitbucket 02 Nov '12

02 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/154cda53407f/ changeset: 154cda53407f user: smcmanus date: 2012-11-02 20:38:54 summary: Temporarily reverted library browsing. affected #: 2 files diff -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 -r 154cda53407f8360ab00b54ec563c1985157c9a5 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -48,7 +48,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/json2")} ${h.js("libs/jquery/jstorage")} ${common_javascripts()} ${self.grid_javascripts()} @@ -207,7 +206,7 @@ </script></%def> -<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"> +<%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"><% ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying @@ -215,14 +214,22 @@ ## library_dataset, so we display the attributes from the ldda. from galaxy.webapps.galaxy.controllers.library_common import branch_deleted - + is_admin = trans.user_is_admin() and cntrller == 'library_admin' - current_version = ( ldda == library_dataset.library_dataset_dataset_association ) + + if ldda == library_dataset.library_dataset_dataset_association: + current_version = True + if is_admin: + can_modify = can_manage = True + elif cntrller in [ 'library', 'requests' ]: + can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset ) + can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset ) + else: + can_modify = can_manage = False + else: + current_version = False if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ): tracked_datasets[ldda.id] = ldda.state - # SM: This causes a query to be emitted, but it quickly goes down a - # rabbit hole of many possible inheritable cases. It may not be - # possible to easily eliminate the extra query from this call. info_association, inherited = ldda.get_info_association( restrict=True ) form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE %> @@ -303,21 +310,9 @@ %endif </%def> -<%def name="format_delta( tdelta )"> - <% - from datetime import datetime - return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds ) - %> -</%def> - <%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )"><% - from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas - - # SM: DELETEME - from datetime import datetime, timedelta - import logging - log = logging.getLogger( __name__ ) + from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted is_admin = trans.user_is_admin() and cntrller == 'library_admin' has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) @@ -330,9 +325,6 @@ pad = folder_pad + 20 expander = h.url_for("/static/images/silk/resultset_next.png") folder_img = h.url_for("/static/images/silk/folder.png") - # SM: If this is a comma-delimited list of LDDAs, then split them up - # into a list. For anything else, turn created_ldda_ids into a single - # item list. if created_ldda_ids: created_ldda_ids = util.listify( created_ldda_ids ) if str( folder.id ) in hidden_folder_ids: @@ -434,39 +426,47 @@ %> %endif <% - # TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case - # in the past. if show_deleted: sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder ) else: sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder ) - # Render all the subfolders: - # TODO: Check permissions first. - for sub_folder in sub_folders: - render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False ) - - # Map LibraryDatasets to LDDAs, then map LDDAs to Datasets. - # Then determine which Datasets are accessible and which are not. - # For every LibraryDataset, if there's an LDDA for it and it's - # accessible then display it. - if ( len( library_datasets ) > 0 ): - lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets ) - dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() ) - #can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list ) - can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list ) - can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list ) - can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list ) - for library_dataset in library_datasets: - ldda = lib_dataset_ldda_map[ library_dataset.id ] - if ldda: - # SMTODO: Fix awkard modify/manage permission checks. - can_access = is_admin or can_access_datasets[ ldda.dataset_id ] - can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ]) - can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ]) + %> + %if is_admin: + %for sub_folder in sub_folders: + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} + %endfor + %for library_dataset in library_datasets: + <% + ldda = library_dataset.library_dataset_dataset_association + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids - if can_access: - render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted ) - %> + %> + %if ldda: + ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} + %endif + %endfor + %else: + %for sub_folder in sub_folders: + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False, simple=simple )} + %endfor + %for library_dataset in library_datasets: + <% + ldda = library_dataset.library_dataset_dataset_association + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + else: + can_access = False + %> + %if can_access: + ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted, simple=simple )} + %endif + %endfor + %endif </%def><%def name="render_content(simple=False)"> @@ -474,8 +474,6 @@ from galaxy import util from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime - import logging - log = logging.getLogger( __name__ ) is_admin = trans.user_is_admin() and cntrller == 'library_admin' @@ -491,8 +489,6 @@ info_association, inherited = library.get_info_association() form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE - # SM: These are mostly display-specific; ignore them for now. - # The has_accessible_folders determines if anything can be shown - use it. self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) @@ -585,16 +581,13 @@ </tr></thead><% row_counter = RowCounter() %> - ## SM: Here is where we render the libraries based on admin/non-admin privileges: %if cntrller in [ 'library', 'requests' ]: ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )} - ## SM: TODO: WTF? %if not library.deleted and self.has_accessible_datasets and not simple: ${render_actions_on_multiple_items()} %endif %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} - ## SM: TODO: WTF? %if not library.deleted and not show_deleted and self.has_accessible_datasets: ${render_actions_on_multiple_items()} %endif diff -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 -r 154cda53407f8360ab00b54ec563c1985157c9a5 templates/library/common/browse_library_opt.mako --- /dev/null +++ b/templates/library/common/browse_library_opt.mako @@ -0,0 +1,622 @@ +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" /> +<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" /> +<%namespace file="/library/common/common.mako" import="render_compression_types_help" /> +<%namespace file="/library/common/common.mako" import="common_javascripts" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/galaxy/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False + self.active_view="user" + self.overlay_visible=False + self.has_accessible_datasets = False +%> +</%def> + +## +## Override methods from base.mako and base_panels.mako +## +<%def name="center_panel()"> + <div style="overflow: auto; height: 100%;"> + <div class="page-container" style="padding: 10px;"> + ${render_content()} + </div> + </div> +</%def> + +## Render the grid's basic elements. Each of these elements can be subclassed. +<%def name="body()"> + ${render_content()} +</%def> + +<%def name="title()">Browse data library</%def> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("libs/json2")} + ${h.js("libs/jquery/jstorage")} + ${common_javascripts()} + ${self.grid_javascripts()} +</%def> + +<%def name="grid_javascripts()"> + <script type="text/javascript"> + var init_libraries = function() { + var storage_id = "library-expand-state-${trans.security.encode_id(library.id)}"; + + var restore_folder_state = function() { + var state = $.jStorage.get(storage_id); + if (state) { + for (var id in state) { + if (state[id] === true) { + var row = $("#" + id), + index = row.parent().children().index(row); + row.addClass("expanded").show(); + row.siblings().filter("tr[parent='" + index + "']").show(); + } + } + } + }; + + var save_folder_state = function() { + var state = {}; + $("tr.folderRow").each( function() { + var folder = $(this); + state[folder.attr("id")] = folder.hasClass("expanded"); + }); + $.jStorage.set(storage_id, state); + }; + + $("#library-grid").each(function() { + var child_of_parent_cache = {}; + // Recursively fill in children and descendents of each row + var process_row = function(q, parents) { + // Find my index + var parent = q.parent(), + this_level = child_of_parent_cache[parent] || (child_of_parent_cache[parent] = parent.children()); + + var index = this_level.index(q); + // Find my immediate children + var children = $(par_child_dict[index]); + // Recursively handle them + var descendents = children; + children.each( function() { + child_descendents = process_row( $(this), parents.add(q) ); + descendents = descendents.add(child_descendents); + }); + // Set up expand / hide link + var expand_fn = function() { + if ( q.hasClass("expanded") ) { + descendents.hide(); + descendents.removeClass("expanded"); + q.removeClass("expanded"); + } else { + children.show(); + q.addClass("expanded"); + } + save_folder_state(); + }; + $("." + q.attr("id") + "-click").click(expand_fn); + // Check/uncheck boxes in subfolders. + q.children("td").children("input[type=checkbox]").click( function() { + if ( $(this).is(":checked") ) { + descendents.find("input[type=checkbox]").attr("checked", true); + } else { + descendents.find("input[type=checkbox]").attr("checked", false); + // If you uncheck a lower level checkbox, uncheck the boxes above it + // (since deselecting a child means the parent is not fully selected any more). + parents.children("td").children("input[type=checkbox]").attr("checked", false); + } + }); + // return descendents for use by parent + return descendents; + } + + // Initialize dict[parent_id] = rows_which_have_that_parent_id_as_parent_attr + var par_child_dict = {}, + no_parent = []; + + $(this).find("tbody tr").each( function() { + if ( $(this).attr("parent")) { + var parent = $(this).attr("parent"); + if (par_child_dict[parent] !== undefined) { + par_child_dict[parent].push(this); + } else { + par_child_dict[parent] = [this]; + } + } else { + no_parent.push(this); + } + }); + + $(no_parent).each( function() { + descendents = process_row( $(this), $([]) ); + descendents.hide(); + }); + }); + + restore_folder_state(); + }; + $(function() { + init_libraries(); + }); + + // Looks for changes in dataset state using an async request. Keeps + // calling itself (via setTimeout) until all datasets are in a terminal + // state. + var updater = function ( tracked_datasets ) { + // Check if there are any items left to track + var empty = true; + for ( i in tracked_datasets ) { + empty = false; + break; + } + if ( ! empty ) { + setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); + } + }; + var updater_callback = function ( tracked_datasets ) { + // Build request data + var ids = [] + var states = [] + $.each( tracked_datasets, function ( id, state ) { + ids.push( id ); + states.push( state ); + }); + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='library_common', action='library_item_updates' )}", + dataType: "json", + data: { ids: ids.join( "," ), states: states.join( "," ) }, + success : function ( data ) { + $.each( data, function( id, val ) { + // Replace HTML + var cell = $("#libraryItem-" + id).find("#libraryItemInfo"); + cell.html( val.html ); + // If new state was terminal, stop tracking + if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { + delete tracked_datasets[ parseInt(id) ]; + } else { + tracked_datasets[ parseInt(id) ] = val.state; + } + }); + updater( tracked_datasets ); + }, + error: function() { + // Just retry, like the old method, should try to be smarter + updater( tracked_datasets ); + } + }); + }; + </script> +</%def> + +<%def name="render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, simple=False )"> + <% + ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods + ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying + ## children, which are always lddas ). We also need to make sure we're displaying the latest version of this + ## library_dataset, so we display the attributes from the ldda. + + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted + + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + current_version = ( ldda == library_dataset.library_dataset_dataset_association ) + if current_version and ldda.state not in ( 'ok', 'error', 'empty', 'deleted', 'discarded' ): + tracked_datasets[ldda.id] = ldda.state + # SM: This causes a query to be emitted, but it quickly goes down a + # rabbit hole of many possible inheritable cases. It may not be + # possible to easily eliminate the extra query from this call. + info_association, inherited = ldda.get_info_association( restrict=True ) + form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + %> + %if current_version and ( not ldda.library_dataset.deleted or show_deleted ): + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${ldda.id}"> + <td style="padding-left: ${pad+20}px;"> + <input style="float: left;" type="checkbox" name="ldda_ids" id="${trans.security.encode_id( ldda.id )}" value="${trans.security.encode_id( ldda.id )}" + %if selected: + checked="checked" + %endif + /> + %if simple: + <label for="${trans.security.encode_id( ldda.id )}">${ util.unicodify( ldda.name )}</label> + %else: + <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup"> + <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}"> + %if ldda.library_dataset.deleted: + <div class="libraryItem-error">${util.unicodify( ldda.name )}</div> + %else: + ${util.unicodify( ldda.name )} + %endif + </a> + </div> + %if not library.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='ldda', item_id=trans.security.encode_id( ldda.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this dataset</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage: + %if not trans.app.security_agent.dataset_is_public( ldda.dataset ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into selected histories</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> + %endif + %if can_modify: + %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: + <a class="action-button" confirm="Click OK to delete dataset '${util.unicodify( ldda.name )}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> + %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %endif + %endif + </div> + %endif + %endif + </td> + % if not simple: + <td id="libraryItemInfo">${render_library_item_info( ldda )}</td> + <td>${ldda.extension}</td> + % endif + <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td> + <td>${ldda.get_size( nice_size=True )}</td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> + %endif +</%def> + +<%def name="format_delta( tdelta )"> + <% + from datetime import datetime + return "%d.%.6d" % ( tdelta.seconds, tdelta.microseconds ) + %> +</%def> + +<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )"> + <% + from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas + + # SM: DELETEME + from datetime import datetime, timedelta + import logging + log = logging.getLogger( __name__ ) + + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) + + if root_folder: + pad = folder_pad + expander = h.url_for("/static/images/silk/resultset_bottom.png") + folder_img = h.url_for("/static/images/silk/folder_page.png") + else: + pad = folder_pad + 20 + expander = h.url_for("/static/images/silk/resultset_next.png") + folder_img = h.url_for("/static/images/silk/folder.png") + # SM: If this is a comma-delimited list of LDDAs, then split them up + # into a list. For anything else, turn created_ldda_ids into a single + # item list. + if created_ldda_ids: + created_ldda_ids = util.listify( created_ldda_ids ) + if str( folder.id ) in hidden_folder_ids: + return "" + my_row = None + if is_admin: + can_add = can_modify = can_manage = True + elif cntrller in [ 'library' ]: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, folder ) + if not can_access: + can_show, folder_ids = \ + trans.app.security_agent.show_library_item( trans.user, + current_user_roles, + folder, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD, + trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, + trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] ) + if not can_show: + return "" + can_add = trans.app.security_agent.can_add_library_item( current_user_roles, folder ) + can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) + can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) + else: + can_add = can_modify = can_manage = False + + form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + info_association, inherited = folder.get_info_association( restrict=True ) + %> + %if not root_folder and ( not folder.deleted or show_deleted ): + <% encoded_id = trans.security.encode_id( folder.id ) %> + <tr id="folder-${encoded_id}" class="folderRow libraryOrFolderRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <td style="padding-left: ${folder_pad}px;"> + <input type="checkbox" class="folderCheckbox"/> + <span class="expandLink folder-${encoded_id}-click"> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> + <a class="folder-${encoded_id}-click" href="javascript:void(0);"> + <span class="rowIcon"></span> + %if folder.deleted: + <div class="libraryItem-error">${folder.name}</div> + %else: + ${folder.name} + %endif + </a> + </div> + </span> + %if not library.deleted: + <div popupmenu="folder_img-${folder.id}-popup"> + %if not branch_deleted( folder ) and can_add: + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> + %endif + %if not branch_deleted( folder ): + %if has_accessible_library_datasets: + <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> + %endif + %if can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='folder', item_id=trans.security.encode_id( folder.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this folder</a> + %else: + <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + %endif + %endif + %if not branch_deleted( folder ) and can_modify and not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a> + %endif + %if not branch_deleted( folder ) and can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', form_type=form_type, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a> + %endif + %if not branch_deleted( folder ) and can_manage: + %if not trans.app.security_agent.folder_is_public( folder ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='folder', id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if can_modify: + %if not library.deleted and not folder.deleted: + <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> + %elif not library.deleted and folder.deleted and not folder.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> + %endif + %endif + </div> + %endif + <td> + %if folder.description: + ${folder.description} + %endif + <td colspan="3"></td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> + %endif + <% + # TODO: If show_deleted is set to True, then nothing is displayed. Why? This wasn't the case + # in the past. + if show_deleted: + sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder ) + else: + sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder ) + # Render all the subfolders: + # TODO: Check permissions first. + for sub_folder in sub_folders: + render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False ) + + # Map LibraryDatasets to LDDAs, then map LDDAs to Datasets. + # Then determine which Datasets are accessible and which are not. + # For every LibraryDataset, if there's an LDDA for it and it's + # accessible then display it. + if ( len( library_datasets ) > 0 ): + lib_dataset_ldda_map = map_library_datasets_to_lddas( trans, library_datasets ) + dataset_list = datasets_for_lddas( trans, lib_dataset_ldda_map.values() ) + #can_access_datasets = trans.app.security_agent.dataset_access_mapping( trans, current_user_roles, dataset_list ) + can_access_datasets = trans.app.security_agent.dataset_permission_map_for_access( trans, current_user_roles, dataset_list ) + can_modify_datasets = trans.app.security_agent.item_permission_map_for_modify( trans, current_user_roles, dataset_list ) + can_manage_datasets = trans.app.security_agent.item_permission_map_for_manage( trans, current_user_roles, dataset_list ) + for library_dataset in library_datasets: + ldda = lib_dataset_ldda_map[ library_dataset.id ] + if ldda: + # SMTODO: Fix awkard modify/manage permission checks. + can_access = is_admin or can_access_datasets[ ldda.dataset_id ] + can_modify = is_admin or ( cntrller in ['library', 'requests'] and can_modify_datasets[ ldda.dataset_id ]) + can_manage = is_admin or ( cntrller in ['library', 'requests'] and can_manage_datasets[ ldda.dataset_id ]) + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + if can_access: + render_dataset( cntrller, ldda, library_dataset, can_modify, can_manage, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted ) + %> +</%def> + +<%def name="render_content(simple=False)"> + <% + from galaxy import util + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted + from time import strftime + import logging + log = logging.getLogger( __name__ ) + + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + + if is_admin: + can_add = can_modify = can_manage = True + elif cntrller in [ 'library', 'requests' ]: + can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library ) + can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) + can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library ) + else: + can_add = can_modify = can_manage = False + + info_association, inherited = library.get_info_association() + form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + + # SM: These are mostly display-specific; ignore them for now. + # The has_accessible_folders determines if anything can be shown - use it. + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) + root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) + has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) + + tracked_datasets = {} + + class RowCounter( object ): + def __init__( self ): + self.count = 0 + def increment( self ): + self.count += 1 + def __str__( self ): + return str( self.count ) + %> + + <h2>Data Library “${library.name}”</h2> + + <ul class="manage-table-actions"> + %if not library.deleted and ( is_admin or can_add ): + <li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a></li> + <li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li> + %endif + %if ( ( not library.deleted ) and ( can_modify or can_manage ) ) or ( can_modify and not library.purged ) or ( library.purged ): + <li><a class="action-button" id="library-${library.id}-popup" class="menubutton">Library Actions</a></li> + <div popupmenu="library-${library.id}-popup"> + %if not library.deleted: + %if can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> + %if show_deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> + %endif + %endif + %if can_modify and not library.info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Use template</a> + %endif + %if can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='library', form_type=form_type, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Unuse template</a> + %endif + %if can_manage: + %if not trans.app.security_agent.library_is_public( library, contents=True ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='library', id=trans.security.encode_id( library.id ), contents=True, use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if root_folder_has_accessible_library_datasets: + <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> + %endif + %elif can_modify and not library.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a> + %elif library.purged: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a> + %endif + </div> + %endif + </ul> + + %if message: + ${render_msg( message, status )} + %endif + + %if library.synopsis not in [ '', 'None', None ]: + <div class="libraryItemBody"> + ${library.synopsis} + </div> + %endif + + %if self.has_accessible_datasets: + <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post"> + %endif + %if has_accessible_folders: + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> + <thead> + <tr class="libraryTitle"> + <th> + %if self.has_accessible_datasets: + <input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/> + %endif + Name + </th> + % if not simple: + <th>Message</th> + <th>Data type</th> + % endif + <th>Date uploaded</th> + <th>File size</th> + </tr> + </thead> + <% row_counter = RowCounter() %> + ## SM: Here is where we render the libraries based on admin/non-admin privileges: + %if cntrller in [ 'library', 'requests' ]: + ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True, simple=simple )} + ## SM: TODO: WTF? + %if not library.deleted and self.has_accessible_datasets and not simple: + ${render_actions_on_multiple_items()} + %endif + %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): + ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} + ## SM: TODO: WTF? + %if not library.deleted and not show_deleted and self.has_accessible_datasets: + ${render_actions_on_multiple_items()} + %endif + %endif + </table> + %endif + %if self.has_accessible_datasets: + </form> + %endif + + %if tracked_datasets: + <script type="text/javascript"> + // Updater + updater({${ ",".join( [ '"%s" : "%s"' % ( k, v ) for k, v in tracked_datasets.iteritems() ] ) }}); + </script> +  + %endif + + %if self.has_accessible_datasets and not simple: + ${render_compression_types_help( comptypes )} + %endif + %if not has_accessible_folders: + The data library '${library.name}' does not contain any datasets that you can access. + %endif +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Cloudlaunch: Automatically detect placement AZ of volumes from existing clusters, and launch using those placements. This prevents any "CRITICAL: This instance must be relaunched in zone..." at cloudman start. Also reworked error handling.
by Bitbucket 01 Nov '12

01 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/59a35ec1e2e7/ changeset: 59a35ec1e2e7 user: dannon date: 2012-11-01 20:39:38 summary: Cloudlaunch: Automatically detect placement AZ of volumes from existing clusters, and launch using those placements. This prevents any "CRITICAL: This instance must be relaunched in zone..." at cloudman start. Also reworked error handling. affected #: 2 files diff -r c42882c539811eac231c5989f89d0dc5f5e3c18e -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -59,14 +59,34 @@ if pd: # This is a cloudman bucket. # We need to get persistent data, and the cluster name. + # DBTODO: Add pyyaml egg, and rewrite this. + # This will also allow for much more sophisticated rendering of existing clusters + # Currently, this zone detection is a hack. + pd_contents = pd.get_contents_as_string() + zone = '' + try: + for line in pd_contents.split('\n'): + if 'vol_id' in line: + vol_id = line.split(':')[1].strip() + v = ec2_conn.get_all_volumes(volume_ids = [vol_id]) + if v: + zone = v[0].zone + else: + zone = '' + except: + #If anything goes wrong with zone detection, use the default selection. + zone = '' for key in bucket.list(): if key.name.endswith('.clusterName'): - clusters.append({'name': key.name.split('.clusterName')[0], 'persistent_data': pd.get_contents_as_string()}) + clusters.append({'name': key.name.split('.clusterName')[0], + 'persistent_data': pd_contents, + 'zone':zone}) account_info['clusters'] = clusters + account_info['zones'] = [z.name for z in ec2_conn.get_all_zones()] return to_json_string(account_info) @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, **kwargs): + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, zone=None, **kwargs): ec2_error = None try: # Create security group & key pair used when starting an instance @@ -90,7 +110,8 @@ rs = run_instance(ec2_conn=ec2_conn, user_provided_data=user_provided_data, key_name=kp_name, - security_groups=[sg_name]) + security_groups=[sg_name], + placement=zone) if rs: instance = rs.instances[0] ct = 0 @@ -241,7 +262,7 @@ def run_instance(ec2_conn, user_provided_data, image_id=DEFAULT_AMI, kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR, - security_groups=['CloudMan']): + placement=None, security_groups=['CloudMan']): """ Start an instance. If instance start was OK, return the ResultSet object else return None. """ @@ -257,7 +278,8 @@ security_groups=security_groups, user_data=ud, kernel_id=kernel_id, - ramdisk_id=ramdisk_id) + ramdisk_id=ramdisk_id, + placement=placement) except EC2ResponseError, e: log.error("Problem starting an instance: %s\n%s" % (e, e.body)) if rs: diff -r c42882c539811eac231c5989f89d0dc5f5e3c18e -r 59a35ec1e2e7ce608d2ae566c7c1e201760c53a1 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -60,6 +60,8 @@ <script type="text/javascript"> var ACCOUNT_URL = "${h.url_for( controller='/cloudlaunch', action='get_account_info')}"; var PKEY_DL_URL = "${h.url_for( controller='/cloudlaunch', action='get_pkey')}"; + var cloudlaunch_clusters = []; + $(document).ready(function(){ $('#id_existing_instance').change(function(){ var ei_name = $(this).val(); @@ -82,6 +84,7 @@ $.getJSON(ACCOUNT_URL, {key_id: key_el.val(),secret:secret_el.val()}, function(result){ + cloudlaunch_clusters = result.clusters; var kplist = $("#id_keypair"); var clusterlist = $("#id_existing_instance"); kplist.find('option').remove(); @@ -112,48 +115,52 @@ $('form').ajaxForm({ type: 'POST', dataType: 'json', - beforeSubmit: function(data){ + beforeSubmit: function(data, form){ if ($('#id_password').val() != $('#id_password_confirm').val()){ //Passwords don't match. - $('#cloudlaunch_form').prepend('<div class="errormessage">Passwords do not match</div>'); + form.prepend('<div class="errormessage">Passwords do not match</div>'); return false; }else{ + //Clear errors $('.errormessage').remove() //Hide the form, show pending box with spinner. $('#launchFormContainer').hide('fast'); $('#responsePanel').show('fast'); } + //Dig up zone info for selected cluster, set hidden input. + //This is not necessary to present to the user though the interface may prove useful. + var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'}); + if( ei_val.value !== "New Cluster"){ + var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value}); + var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'}); + zdata.value = cluster.zone; + } }, success: function(data){ //Success Message, link to key download if required, link to server itself. $('#launchPending').hide('fast'); - //Check for success/error. - if (data.error){ - //Apologize profusely. - $("launchPending").hide(); - $("#launchError").show(); - }else{ - //Set appropriate fields (dns, key, ami) and then display. - if(data.kp_material_tag){ - var kp_download_link = $('<a/>').attr('href', PKEY_DL_URL + '?kp_material_tag=' + data.kp_material_tag) - .attr('target','_blank') - .text("Download your key now"); - $('#keypairInfo').append(kp_download_link); - $('#keypairInfo').show(); - } - $('.kp_name').text(data.kp_name); - $('#instance_id').text(data.instance_id); - $('#image_id').text(data.image_id); - $('#instance_link').html($('<a/>') - .attr('href', 'http://' + data.public_dns_name + '/cloud') - .attr('target','_blank') - .text(data.public_dns_name + '/cloud')); - $('#instance_dns').text(data.public_dns_name); - $('#launchSuccess').show('fast'); + //Set appropriate fields (dns, key, ami) and then display. + if(data.kp_material_tag){ + var kp_download_link = $('<a/>').attr('href', PKEY_DL_URL + '?kp_material_tag=' + data.kp_material_tag) + .attr('target','_blank') + .text("Download your key now"); + $('#keypairInfo').append(kp_download_link); + $('#keypairInfo').show(); } + $('.kp_name').text(data.kp_name); + $('#instance_id').text(data.instance_id); + $('#image_id').text(data.image_id); + $('#instance_link').html($('<a/>') + .attr('href', 'http://' + data.public_dns_name + '/cloud') + .attr('target','_blank') + .text(data.public_dns_name + '/cloud')); + $('#instance_dns').text(data.public_dns_name); + $('#launchSuccess').show('fast'); }, - error: function(data){ - $('#cloudlaunch_form').prepend('<div class="errormessage">' + data.responseText + '</div>'); + error: function(jqXHR, textStatus, errorThrown){ + $('#launchFormContainer').prepend('<div class="errormessage">' + errorThrown + " : " + jqXHR.responseText + '</div>'); + $('#responsePanel').hide('fast'); + $('#launchFormContainer').show('fast'); } }); }); @@ -196,6 +203,7 @@ <label for="id_existing_instance">Instances in your account</label><select name="existing_instance" id="id_existing_instance"></select> + <input id='id_zone' type='hidden' name='zone' value=''/></div><div id='cluster_name_wrapper' class="form-row"><label for="id_cluster_name">Cluster Name</label> @@ -253,7 +261,6 @@ </div><div id="responsePanel" class="toolForm" style="display:none;"><div id="launchPending">Launch Pending, please be patient.</div> - <div id="launchError" style="display:none;">ERROR</div><div id="launchSuccess" style="display:none;"><div id="keypairInfo" style="display:none;margin-bottom:20px;"><h3>Very Important Key Pair Information</h3> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Pack scripts.
by Bitbucket 01 Nov '12

01 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c42882c53981/ changeset: c42882c53981 user: jgoecks date: 2012-11-01 18:27:07 summary: Pack scripts. affected #: 2 files diff -r 014fee888b86f0c2f250cbe60ae9dfda9d0077a0 -r c42882c539811eac231c5989f89d0dc5f5e3c18e static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/visualization"],function(g,k,h){var l=Backbone.Model.extend({is_visible:function(p,m){var n=p.getBoundingClientRect(),o=$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var c=Backbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var a=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=20;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(m){return m.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(m){return m.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var n=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-n.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=k.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var m=this;return g.map(tracks_start_radii,function(o){return[o,o+m.dataset_arc_height]})},render:function(){var u=this,p=this.dataset_arc_height,m=u.$el.width(),t=u.$el.height(),r=this.get_circular_tracks(),o=this.get_chord_tracks(),q=this.get_tracks_bounds(),n=k.select(u.$el[0]).append("svg").attr("width",m).attr("height",t).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){var v=k.event.scale;n.attr("transform","translate("+k.event.translate+") scale("+v+")");if(u.scale!==v){if(u.zoom_drag_timeout){clearTimeout(u.zoom_drag_timeout)}u.zoom_drag_timeout=setTimeout(function(){g.each(u.circular_views,function(w){w.update_scale(v)})},400)}})).attr("transform","translate("+m/2+","+t/2+")").append("svg:g").attr("class","tracks");this.circular_views=r.map(function(w,x){var y=(w.get("track_type")==="LineTrack"?d:e),v=new y({el:n.append("g")[0],track:w,radius_bounds:q[x],genome:u.genome,total_gap:u.total_gap});v.render();return v});this.chords_views=o.map(function(w){var v=new i({el:n.append("g")[0],track:w,radius_bounds:q[0],genome:u.genome,total_gap:u.total_gap});v.render();return v});var s=q[r.length];s[1]=s[0];this.label_track_view=new b({el:n.append("g")[0],track:new c(),radius_bounds:s,genome:u.genome,total_gap:u.total_gap});this.label_track_view.render()},add_track:function(s){if(s.get("track_type")==="DiagonalHeatmapTrack"){var o=this.circular_views[0].radius_bounds,r=new i({el:k.select("g.tracks").append("g")[0],track:s,radius_bounds:o,genome:this.genome,total_gap:this.total_gap});r.render();this.chords_views.push(r)}else{var q=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(q[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(q[0])});var p=this.circular_views.length,t=(s.get("track_type")==="LineTrack"?d:e),m=new t({el:k.select("g.tracks").append("g")[0],track:s,radius_bounds:q[p],genome:this.genome,total_gap:this.total_gap});m.render();this.circular_views.push(m);var n=q[q.length-1];n[1]=n[0];this.label_track_view.update_radius_bounds(n)}},remove_track:function(n,p,o){var m=this.circular_views[o.index];this.circular_views.splice(o.index,1);m.$el.remove();var q=this.get_tracks_bounds();g.each(this.circular_views,function(r,s){r.update_radius_bounds(q[s])})}});var j=Backbone.View.extend({tagName:"g",initialize:function(m){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=m.total_gap;this.track=m.track;this.radius_bounds=m.radius_bounds;this.genome=m.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=k.select(this.$el[0])},get_fill_color:function(){var m=this.track.get("config").get_value("block_color");if(!m){m=this.track.get("config").get_value("color")}return m},render:function(){var q=this.parent_elt;if(!q){console.log("no parent elt")}var p=this.chroms_layout,s=k.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),m=q.selectAll("g").data(p).enter().append("svg:g"),o=m.append("path").attr("d",s).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);o.append("title").text(function(u){return u.data.chrom});var n=this,r=n.track.get("data_manager"),t=(r?r.data_is_ready():true);$.when(t).then(function(){$.when(n._render_data(q)).then(function(){o.style("fill",n.bg_fill)})})},update_radius_bounds:function(n){this.radius_bounds=n;var m=k.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",m);this._transition_chrom_data()},update_scale:function(p){var o=this.scale;this.scale=p;if(p<=o){return}var n=this,m=new l();this.parent_elt.selectAll("path.chrom-data").filter(function(r,q){return m.is_visible(this)}).each(function(w,s){var v=k.select(this),r=v.attr("chrom"),u=n.genome.get_chrom_region(r),t=n.track.get("data_manager"),q;if(!t.can_get_more_detailed_data(u)){return}q=n.track.get("data_manager").get_more_detailed_data(u,"Coverage",0,p);$.when(q).then(function(z){v.remove();n._update_data_bounds();var y=g.find(n.chroms_layout,function(A){return A.data.chrom===r});var x=n.get_fill_color();n._render_chrom_data(n.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_transition_chrom_data:function(){var n=this.track,p=this.chroms_layout,m=this.parent_elt.selectAll("g>path.chrom-data"),q=m[0].length;if(q>0){var o=this;$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){var r=g.reject(g.map(s,function(t,u){var v=null,w=o._get_path_function(p[u],t);if(w){v=w(t.data)}return v}),function(t){return t===null});m.each(function(u,t){k.select(this).transition().duration(1000).attr("d",r[t])})})}},_update_data_bounds:function(){var m=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<m[0]||this.data_bounds[1]>m[1]){this._transition_chrom_data()}},_render_data:function(p){var o=this,n=this.chroms_layout,m=this.track,q=$.Deferred();$.when(m.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){o.data_bounds=o.get_data_bounds(s);layout_and_data=g.zip(n,s),chroms_data_layout=g.map(layout_and_data,function(t){var u=t[0],v=t[1];return o._render_chrom_data(p,u,v)});var r=o.get_fill_color();o.parent_elt.selectAll("path.chrom-data").style("stroke",r).style("fill",r);q.resolve(p)});return q},_render_chrom_data:function(m,n,o){},_get_path_function:function(n,m){},_chroms_layout:function(){var n=this.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.total_gap/n.length,o=g.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o}});var b=j.extend({initialize:function(m){j.prototype.initialize.call(this,m);this.bg_stroke="fff";this.bg_fill="fff"},_render_data:function(n){var m=n.selectAll("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom});m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0.08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(function(o){return o.data.chrom})}});var f=j.extend({_render_chrom_data:function(m,p,n){var q=this._get_path_function(p,n);if(!q){return null}var o=m.datum(n.data),r=o.append("path").attr("class","chrom-data").attr("chrom",p.data.chrom).attr("d",q);return r},_get_path_function:function(p,o){if(typeof o==="string"||!o.data||o.data.length===0){return null}var m=k.scale.linear().domain(this.data_bounds).range(this.radius_bounds);var q=k.scale.linear().domain([0,o.data.length]).range([p.startAngle,p.endAngle]);var n=k.svg.line.radial().interpolate("linear").radius(function(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.radial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius()).angle(n.angle())},get_data_bounds:function(m){}});var e=f.extend({get_data_bounds:function(n){var m=g.map(n,function(o){if(typeof o==="string"||!o.max){return 0}return o.max});return[0,(m&&typeof m!=="string"?g.max(m):0)]}});var d=f.extend({get_data_bounds:function(n){var m=g.flatten(g.map(n,function(o){if(o){return g.map(o.data,function(q){return q[1]})}else{return 0}}));return[g.min(m),g.max(m)]}});var i=j.extend({render:function(){var m=this;$.when(m.track.get("data_manager").data_is_ready()).then(function(){$.when(m.track.get("data_manager").get_genome_wide_data(m.genome)).then(function(p){var o=[],n=m.genome.get_chroms_info();g.each(p,function(t,s){var q=n[s].chrom;var r=g.map(t.data,function(v){var u=m._get_region_angle(q,v[1]),w=m._get_region_angle(v[3],v[4]);return{source:{startAngle:u,endAngle:u+0.01},target:{startAngle:w,endAngle:w+0.01}}});o=o.concat(r)});m.parent_elt.append("g").attr("class","chord").selectAll("path").data(o).enter().append("path").style("fill",m.get_fill_color()).attr("d",k.svg.chord().radius(m.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(m){this.radius_bounds=m;this.parent_elt.selectAll("path").transition().attr("d",k.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(o,m){var n=g.find(this.chroms_layout,function(p){return p.data.chrom===o});return n.endAngle-((n.endAngle-n.startAngle)*(n.data.len-m)/n.data.len)}});return{CircsterView:a}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,k,h){var l=Backbone.Model.extend({is_visible:function(p,m){var n=p.getBoundingClientRect(),o=$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(m){return m.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(m){return m.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var n=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-n.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=k.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var m=this;return g.map(tracks_start_radii,function(o){return[o,o+m.dataset_arc_height]})},render:function(){var v=this,p=this.dataset_arc_height,m=v.$el.width(),u=v.$el.height(),r=this.get_circular_tracks(),o=this.get_chord_tracks(),q=this.get_tracks_bounds(),n=k.select(v.$el[0]).append("svg").attr("width",m).attr("height",u).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){var w=k.event.scale;n.attr("transform","translate("+k.event.translate+") scale("+w+")");if(v.scale!==w){if(v.zoom_drag_timeout){clearTimeout(v.zoom_drag_timeout)}v.zoom_drag_timeout=setTimeout(function(){g.each(v.circular_views,function(x){x.update_scale(w)})},400)}})).attr("transform","translate("+m/2+","+u/2+")").append("svg:g").attr("class","tracks");this.circular_views=r.map(function(x,y){var z=(x.get("track_type")==="LineTrack"?d:e),w=new z({el:n.append("g")[0],track:x,radius_bounds:q[y],genome:v.genome,total_gap:v.total_gap});w.render();return w});this.chords_views=o.map(function(x){var w=new i({el:n.append("g")[0],track:x,radius_bounds:q[0],genome:v.genome,total_gap:v.total_gap});w.render();return w});var t=this.circular_views[this.circular_views.length-1].radius_bounds[1],s=[t,t+this.label_arc_height];this.label_track_view=new b({el:n.append("g")[0],track:new c(),radius_bounds:s,genome:v.genome,total_gap:v.total_gap});this.label_track_view.render()},add_track:function(s){if(s.get("track_type")==="DiagonalHeatmapTrack"){var o=this.circular_views[0].radius_bounds,r=new i({el:k.select("g.tracks").append("g")[0],track:s,radius_bounds:o,genome:this.genome,total_gap:this.total_gap});r.render();this.chords_views.push(r)}else{var q=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(q[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(q[0])});var p=this.circular_views.length,t=(s.get("track_type")==="LineTrack"?d:e),m=new t({el:k.select("g.tracks").append("g")[0],track:s,radius_bounds:q[p],genome:this.genome,total_gap:this.total_gap});m.render();this.circular_views.push(m);var n=q[q.length-1];n[1]=n[0];this.label_track_view.update_radius_bounds(n)}},remove_track:function(n,p,o){var m=this.circular_views[o.index];this.circular_views.splice(o.index,1);m.$el.remove();var q=this.get_tracks_bounds();g.each(this.circular_views,function(r,s){r.update_radius_bounds(q[s])})}});var j=Backbone.View.extend({tagName:"g",initialize:function(m){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=m.total_gap;this.track=m.track;this.radius_bounds=m.radius_bounds;this.genome=m.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=k.select(this.$el[0])},get_fill_color:function(){var m=this.track.get("config").get_value("block_color");if(!m){m=this.track.get("config").get_value("color")}return m},render:function(){var q=this.parent_elt;if(!q){console.log("no parent elt")}var p=this.chroms_layout,s=k.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),m=q.selectAll("g").data(p).enter().append("svg:g"),o=m.append("path").attr("d",s).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);o.append("title").text(function(u){return u.data.chrom});var n=this,r=n.track.get("data_manager"),t=(r?r.data_is_ready():true);$.when(t).then(function(){$.when(n._render_data(q)).then(function(){o.style("fill",n.bg_fill)})})},update_radius_bounds:function(n){this.radius_bounds=n;var m=k.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",m);this._transition_chrom_data()},update_scale:function(p){var o=this.scale;this.scale=p;if(p<=o){return}var n=this,m=new l();this.parent_elt.selectAll("path.chrom-data").filter(function(r,q){return m.is_visible(this)}).each(function(w,s){var v=k.select(this),r=v.attr("chrom"),u=n.genome.get_chrom_region(r),t=n.track.get("data_manager"),q;if(!t.can_get_more_detailed_data(u)){return}q=n.track.get("data_manager").get_more_detailed_data(u,"Coverage",0,p);$.when(q).then(function(z){v.remove();n._update_data_bounds();var y=g.find(n.chroms_layout,function(A){return A.data.chrom===r});var x=n.get_fill_color();n._render_chrom_data(n.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_transition_chrom_data:function(){var n=this.track,p=this.chroms_layout,m=this.parent_elt.selectAll("g>path.chrom-data"),q=m[0].length;if(q>0){var o=this;$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){var r=g.reject(g.map(s,function(t,u){var v=null,w=o._get_path_function(p[u],t);if(w){v=w(t.data)}return v}),function(t){return t===null});m.each(function(u,t){k.select(this).transition().duration(1000).attr("d",r[t])})})}},_update_data_bounds:function(){var m=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<m[0]||this.data_bounds[1]>m[1]){this._transition_chrom_data()}},_render_data:function(p){var o=this,n=this.chroms_layout,m=this.track,q=$.Deferred();$.when(m.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){o.data_bounds=o.get_data_bounds(s);layout_and_data=g.zip(n,s),chroms_data_layout=g.map(layout_and_data,function(t){var u=t[0],v=t[1];return o._render_chrom_data(p,u,v)});var r=o.get_fill_color();o.parent_elt.selectAll("path.chrom-data").style("stroke",r).style("fill",r);q.resolve(p)});return q},_render_chrom_data:function(m,n,o){},_get_path_function:function(n,m){},_chroms_layout:function(){var n=this.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.total_gap/n.length,o=g.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o}});var b=j.extend({initialize:function(m){j.prototype.initialize.call(this,m);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(o){var n=this,m=o.selectAll("g");m.selectAll("path").attr("id",function(r){return"label-"+r.data.chrom});m.append("svg:text").filter(function(r){return r.endAngle-r.startAngle>n.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(r){return"#label-"+r.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(r){return r.data.chrom});var q=function(t){if(t.endAngle-t.startAngle<n.min_arc_len){return[]}var r=(t.endAngle-t.startAngle)/t.value,s=k.range(0,t.value,25000000).map(function(u,w){return{angle:u*r+t.startAngle,label:w===0?0:(w%3?null:u/1000000+"M")}});if(s.length<4){s[s.length-1].label=Math.round((s[s.length-1].angle-t.startAngle)/r/1000000)+"M"}return s};var p=this.parent_elt.append("g").selectAll("g").data(this.chroms_layout).enter().append("g").selectAll("g").data(q).enter().append("g").attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+n.innerRadius+",0)"});p.append("line").attr("x1",1).attr("y1",0).attr("x2",4).attr("y2",0).style("stroke","#000");p.append("text").attr("x",4).attr("dy",".35em").attr("text-anchor",function(r){return r.angle>Math.PI?"end":null}).attr("transform",function(r){return r.angle>Math.PI?"rotate(180)translate(-16)":null}).text(function(r){return r.label})}});var f=j.extend({_render_chrom_data:function(m,p,n){var q=this._get_path_function(p,n);if(!q){return null}var o=m.datum(n.data),r=o.append("path").attr("class","chrom-data").attr("chrom",p.data.chrom).attr("d",q);return r},_get_path_function:function(p,o){if(typeof o==="string"||!o.data||o.data.length===0){return null}var m=k.scale.linear().domain(this.data_bounds).range(this.radius_bounds);var q=k.scale.linear().domain([0,o.data.length]).range([p.startAngle,p.endAngle]);var n=k.svg.line.radial().interpolate("linear").radius(function(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.radial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius()).angle(n.angle())},get_data_bounds:function(m){}});var e=f.extend({get_data_bounds:function(n){var m=g.map(n,function(o){if(typeof o==="string"||!o.max){return 0}return o.max});return[0,(m&&typeof m!=="string"?g.max(m):0)]}});var d=f.extend({get_data_bounds:function(n){var m=g.flatten(g.map(n,function(o){if(o){return g.map(o.data,function(q){return q[1]})}else{return 0}}));return[g.min(m),g.max(m)]}});var i=j.extend({render:function(){var m=this;$.when(m.track.get("data_manager").data_is_ready()).then(function(){$.when(m.track.get("data_manager").get_genome_wide_data(m.genome)).then(function(p){var o=[],n=m.genome.get_chroms_info();g.each(p,function(t,s){var q=n[s].chrom;var r=g.map(t.data,function(v){var u=m._get_region_angle(q,v[1]),w=m._get_region_angle(v[3],v[4]);return{source:{startAngle:u,endAngle:u+0.01},target:{startAngle:w,endAngle:w+0.01}}});o=o.concat(r)});m.parent_elt.append("g").attr("class","chord").selectAll("path").data(o).enter().append("path").style("fill",m.get_fill_color()).attr("d",k.svg.chord().radius(m.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(m){this.radius_bounds=m;this.parent_elt.selectAll("path").transition().attr("d",k.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(o,m){var n=g.find(this.chroms_layout,function(p){return p.data.chrom===o});return n.endAngle-((n.endAngle-n.startAngle)*(n.data.len-m)/n.data.len)}});return{CircsterView:a}}); \ No newline at end of file diff -r 014fee888b86f0c2f250cbe60ae9dfda9d0077a0 -r c42882c539811eac231c5989f89d0dc5f5e3c18e static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.set_dataset(new Y.Dataset(aj));ai.tiles_div.text("Running job.");ai.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),ae={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(af.message){var ag=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+af.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(ag)}}else{if(af==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(af==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ad.valid_chroms=af.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*S*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(ae,af,ah,ac){var ag=false;for(var ad=0;ad<ae.length;ad++){if(ae[ad].has_icons){ag=true;break}}if(ag){for(var ad=0;ad<ae.length;ad++){tile=ae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar);if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}}if(al){q(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),av=af.get("start"),ad=af.get("end"),ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!==undefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=this,aD=this._gen_tile_cache_key(at,am,az),ah=this._get_tile_bounds(az,aw);if(!au){au={}}var aC=(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC,ak,am);return aC}var al=[],ar,ap=true,ax,an;for(var ay=0;ay<this.drawables.length;ay++){ar=this.drawables[ay];ax=ar.data_manager.get_data(ah,ar.mode,aw,ar.data_url_extra_params);if(V(ax)){ap=false}al.push(ax);an=null;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=view.reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_track.data_url_extra_params);if(V(an)){ap=false}}al.push(an)}if(ap){q(ax,au.more_tile_data);this.tile_predraw_init();var ag=ar.view.canvas_manager.new_canvas(),ai=ar._get_tile_bounds(az,aw),aA=ah.get("start"),ae=ah.get("end"),aB=0,at=Math.ceil((ae-aA)*am)+this.left_offset,aq=0,af=[],ay;var ac=0;for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];var ao=ar.mode;if(ao==="Auto"){ao=ar.get_mode(ax);ar.update_auto_mode(ao)}af.push(ao);ac=ar.get_canvas_height(ax,ao,am,at);if(ac>aq){aq=ac}}ag.width=at;ag.height=(au.height?au.height:aq);aB=0;var av=ag.getContext("2d");av.translate(this.left_offset,0);av.globalAlpha=0.5;av.globalCompositeOperation="source-over";for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];an=al[aB+1];aC=ar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache.set_elt(aD,aC);this.show_tile(aC,ak,am);return aC}var aj=$.Deferred(),ar=this;$.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar);aj.resolve()});return aj},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah,ai,af){if(ai>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return null}},draw_tile:function(ak,al,ag,af,ai,am){var ae=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ah=0,aj=ak.length;ah<aj;ah++){var ac=Math.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();return new b(ae,ai,af,ad,ak)}this.hide_contents()}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return false}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.set_dataset(new Y.Dataset(aj));ai.tiles_div.text("Running job.");ai.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*S*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(ae,af,ah,ac){var ag=false;for(var ad=0;ad<ae.length;ad++){if(ae[ad].has_icons){ag=true;break}}if(ag){for(var ad=0;ad<ae.length;ad++){tile=ae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar);if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}}if(al){q(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),av=af.get("start"),ad=af.get("end"),ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!==undefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=this,aD=this._gen_tile_cache_key(at,am,az),ah=this._get_tile_bounds(az,aw);if(!au){au={}}var aC=(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC,ak,am);return aC}var al=[],ar,ap=true,ax,an;for(var ay=0;ay<this.drawables.length;ay++){ar=this.drawables[ay];ax=ar.data_manager.get_data(ah,ar.mode,aw,ar.data_url_extra_params);if(V(ax)){ap=false}al.push(ax);an=null;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=view.reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_track.data_url_extra_params);if(V(an)){ap=false}}al.push(an)}if(ap){q(ax,au.more_tile_data);this.tile_predraw_init();var ag=ar.view.canvas_manager.new_canvas(),ai=ar._get_tile_bounds(az,aw),aA=ah.get("start"),ae=ah.get("end"),aB=0,at=Math.ceil((ae-aA)*am)+this.left_offset,aq=0,af=[],ay;var ac=0;for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];var ao=ar.mode;if(ao==="Auto"){ao=ar.get_mode(ax);ar.update_auto_mode(ao)}af.push(ao);ac=ar.get_canvas_height(ax,ao,am,at);if(ac>aq){aq=ac}}ag.width=at;ag.height=(au.height?au.height:aq);aB=0;var av=ag.getContext("2d");av.translate(this.left_offset,0);av.globalAlpha=0.5;av.globalCompositeOperation="source-over";for(ay=0;ay<this.drawables.length;ay++,aB+=2){ar=this.drawables[ay];ax=al[aB];an=al[aB+1];aC=ar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache.set_elt(aD,aC);this.show_tile(aC,ak,am);return aC}var aj=$.Deferred(),ar=this;$.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar);aj.resolve()});return aj},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah,ai,af){if(ai>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return null}},draw_tile:function(ak,al,ag,af,ai,am){var ae=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ah=0,aj=ak.length;ah<aj;ah++){var ac=Math.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();return new b(ae,ai,af,ad,ak)}this.hide_contents()}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return false}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Provide option to retry dataset indexing/conversion in Trackster. Also, move is_true method into Web helpers for general access.
by Bitbucket 01 Nov '12

01 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/014fee888b86/ changeset: 014fee888b86 user: jgoecks date: 2012-11-01 15:04:12 summary: Provide option to retry dataset indexing/conversion in Trackster. Also, move is_true method into Web helpers for general access. affected #: 4 files diff -r 5440f6b3bdecf081493aa31f473470fd11fecceb -r 014fee888b86f0c2f250cbe60ae9dfda9d0077a0 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -90,4 +90,11 @@ return unicode( a_string, 'utf-8' ) elif a_string_type is unicode: return a_string + +def is_true ( val ): + """ + Returns true if input is a boolean and true or is a string and looks like a true value. + """ + return val == True or val in [ 'True', 'true', 'T', 't' ] + \ No newline at end of file diff -r 5440f6b3bdecf081493aa31f473470fd11fecceb -r 014fee888b86f0c2f250cbe60ae9dfda9d0077a0 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -11,6 +11,7 @@ from galaxy.visualization.data_providers.basic import ColumnDataProvider from galaxy.datatypes.tabular import Vcf from galaxy.model import NoConverterException, ConverterDependencyException +from galaxy.web.framework.helpers import is_true log = logging.getLogger( __name__ ) @@ -42,7 +43,8 @@ if data_type == 'state': rval = self._dataset_state( trans, dataset ) elif data_type == 'converted_datasets_state': - rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ) ) + rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ), + is_true( kwd.get( 'retry', False ) ) ) elif data_type == 'data': rval = self._data( trans, dataset, **kwd ) elif data_type == 'features': @@ -72,22 +74,26 @@ return msg - def _converted_datasets_state( self, trans, dataset, chrom=None ): + def _converted_datasets_state( self, trans, dataset, chrom=None, retry=False ): """ - Init-like method that returns state of dataset's converted datasets. Returns valid chroms - for that dataset as well. + Init-like method that returns state of dataset's converted datasets. + Returns valid chroms for that dataset as well. """ - msg = self.check_dataset_state( trans, dataset ) if msg: return msg - # Get datasources and check for messages. + # Get datasources and check for messages (which indicate errors). Retry if flag is set. data_sources = dataset.get_datasources( trans ) messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] msg = get_highest_priority_msg( messages_list ) if msg: - return msg + if retry: + # Clear datasources and then try again. + dataset.clear_associated_files() + return self._converted_datasets_state( trans, dataset, chrom ) + else: + return msg # If there is a chrom, check for data on the chrom. if chrom: diff -r 5440f6b3bdecf081493aa31f473470fd11fecceb -r 014fee888b86f0c2f250cbe60ae9dfda9d0077a0 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -1,9 +1,7 @@ from galaxy import config, tools, web, util from galaxy.web.base.controller import BaseController, BaseAPIController from galaxy.util.bunch import Bunch - -def is_true ( a_str ): - return is_true == True or a_str in [ 'True', 'true', 'T', 't' ] +from galaxy.web.framework.helpers import is_true def get_id( base, format ): if format: diff -r 5440f6b3bdecf081493aa31f473470fd11fecceb -r 014fee888b86f0c2f250cbe60ae9dfda9d0077a0 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -170,7 +170,7 @@ DEFAULT_DATA_QUERY_WAIT = 5000, // Maximum number of chromosomes that are selectable at any one time. MAX_CHROMS_SELECTABLE = 100, - DATA_ERROR = "There was an error in indexing this dataset. ", + DATA_ERROR = "Cannot display dataset due to an error. ", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Preparing data. This can take a while for a large dataset. " + @@ -2513,7 +2513,7 @@ /** * Initialize and draw the track. */ - init: function() { + init: function(retry) { var track = this; track.enabled = false; track.tile_cache.clear(); @@ -2525,7 +2525,7 @@ } */ // Remove old track content (e.g. tiles, messages). - track.tiles_div.children().remove(); + track.tiles_div.text('').children().remove(); track.container_div.removeClass("nodata error pending"); // @@ -2542,16 +2542,27 @@ params = { hda_ldda: track.hda_ldda, data_type: this.dataset_check_type, - chrom: track.view.chrom }; + chrom: track.view.chrom, + retry: retry + }; $.getJSON(this.dataset.url(), params, function (result) { if (!result || result === "error" || result.kind === "error") { + // Dataset is in error state. track.container_div.addClass("error"); track.tiles_div.text(DATA_ERROR); if (result.message) { - var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").click(function() { - show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); - }); - track.tiles_div.append(error_link); + // Add links to (a) show error and (b) try again. + track.tiles_div.append( + $("<a href='javascript:void(0);'></a>").text("View error").click(function() { + show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); + }) + ); + track.tiles_div.append( $('<span/>').text(' ') ); + track.tiles_div.append( + $("<a href='javascript:void(0);'></a>").text("Try again").click(function() { + track.init(true); + }) + ); } } else if (result === "no converter") { track.container_div.addClass("error"); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Viz framework: (a) add option to store open file reference in data providers rather than recreating each time and (b) add ticks marks in Circster for chromosome lengths.
by Bitbucket 31 Oct '12

31 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5440f6b3bdec/ changeset: 5440f6b3bdec user: jgoecks date: 2012-10-31 22:51:38 summary: Viz framework: (a) add option to store open file reference in data providers rather than recreating each time and (b) add ticks marks in Circster for chromosome lengths. affected #: 3 files diff -r 8526b10ca125a99de4d944e776e647c1598ffd06 -r 5440f6b3bdecf081493aa31f473470fd11fecceb lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -130,6 +130,11 @@ original_dataset=original_dataset, dependencies=dependencies, error_max_vals=error_max_vals ) + + # File/pointer where data is obtained from. It is useful to set this for repeated + # queries, such as is necessary for genome-wide data. + # TODO: add functions to (a) create data_file and (b) clean up data_file. + self.data_file = None def write_data_to_file( self, regions, filename ): """ @@ -345,17 +350,18 @@ bgzip_fname = self.dependencies['bgzip'].file_name - tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) + if not self.data_file: + self.data_file = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) # Get iterator using either naming scheme. iterator = iter( [] ) - if chrom in tabix.contigs: - iterator = tabix.fetch(reference=chrom, start=start, end=end) + if chrom in self.data_file.contigs: + iterator = self.data_file.fetch(reference=chrom, start=start, end=end) else: # Try alternative naming scheme. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - if chrom in tabix.contigs: - iterator = tabix.fetch(reference=chrom, start=start, end=end) + if chrom in self.data_file.contigs: + iterator = self.data_file.fetch(reference=chrom, start=start, end=end) return iterator diff -r 8526b10ca125a99de4d944e776e647c1598ffd06 -r 5440f6b3bdecf081493aa31f473470fd11fecceb lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -110,5 +110,8 @@ cPickle.dump( self, open( filename, 'wb' ), 2 ) def summary_tree_from_file( filename ): - return cPickle.load( open( filename, "rb" ) ) + st_file = open( filename, "rb" ) + st = cPickle.load( st_file ) + st_file.close() + return st diff -r 8526b10ca125a99de4d944e776e647c1598ffd06 -r 5440f6b3bdecf081493aa31f473470fd11fecceb static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -27,13 +27,7 @@ /** * A label track. */ -var CircsterLabelTrack = Backbone.Model.extend({ - defaults: { - prefs: { - color: '#ccc' - } - } -}); +var CircsterLabelTrack = Backbone.Model.extend({}); /** * Renders a full circster visualization. @@ -46,7 +40,7 @@ this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; - this.label_arc_height = 20; + this.label_arc_height = 50; this.scale = 1; this.circular_views = null; this.chords_views = null; @@ -78,7 +72,7 @@ }, /** - * Returns a list of tracks' radius bounds. + * Returns a list of circular tracks' radius bounds. */ get_tracks_bounds: function() { var circular_tracks = this.get_circular_tracks(); @@ -93,7 +87,7 @@ // Compute range of track starting radii. tracks_start_radii = d3.range(radius_start, min_dimension / 2, this.dataset_arc_height + this.track_gap); - // Map from track start to bounds; for label track + // Map from track start to bounds. var self = this; return _.map(tracks_start_radii, function(radius) { return [radius, radius + self.dataset_arc_height]; @@ -180,12 +174,17 @@ return view; }); - // -- Render label tracks. -- + // -- Render label track. -- - // Set radius start = end for track bounds. - var track_bounds = tracks_bounds[circular_tracks.length]; - track_bounds[1] = track_bounds[0]; - this.label_track_view = new CircsterLabelTrackView({ + // Track bounds are: + // (a) outer radius of last circular track; + // (b) + var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1], + track_bounds = [ + outermost_radius, + outermost_radius + this.label_arc_height + ]; + this.label_track_view = new CircsterChromLabelTrackView({ el: svg.append('g')[0], track: new CircsterLabelTrack(), radius_bounds: track_bounds, @@ -534,36 +533,97 @@ /** * Render chromosome labels. */ -var CircsterLabelTrackView = CircsterTrackView.extend({ +var CircsterChromLabelTrackView = CircsterTrackView.extend({ initialize: function(options) { CircsterTrackView.prototype.initialize.call(this, options); + // Use a single arc for rendering data. + this.innerRadius = this.radius_bounds[0]; + this.radius_bounds[0] = this.radius_bounds[1]; this.bg_stroke = 'fff'; this.bg_fill = 'fff'; + + // Minimum arc distance for labels to be applied. + this.min_arc_len = 0.08; }, /** * Render labels. */ _render_data: function(svg) { - // Add chromosome label where it will fit; an alternative labeling mechanism - // would be nice for small chromosomes. - var chrom_arcs = svg.selectAll('g'); + // -- Add chromosome label where it will fit; an alternative labeling mechanism + // would be nice for small chromosomes. -- + var self = this, + chrom_arcs = svg.selectAll('g'); chrom_arcs.selectAll('path') .attr('id', function(d) { return 'label-' + d.data.chrom; }); chrom_arcs.append("svg:text") .filter(function(d) { - return d.endAngle - d.startAngle > 0.08; + return d.endAngle - d.startAngle > self.min_arc_len; }) .attr('text-anchor', 'middle') .append("svg:textPath") .attr("xlink:href", function(d) { return "#label-" + d.data.chrom; }) .attr('startOffset', '25%') + .attr('font-weight', 'bold') .text(function(d) { return d.data.chrom; }); + + // -- Add ticks to denote chromosome length. -- + + /** Returns an array of tick angles and labels, given a chrom arc. */ + var chromArcTicks = function(d) { + if (d.endAngle - d.startAngle < self.min_arc_len) { return []; } + var k = (d.endAngle - d.startAngle) / d.value, + ticks = d3.range(0, d.value, 25000000).map(function(v, i) { + return { + angle: v * k + d.startAngle, + label: i === 0 ? 0 : (i % 3 ? null : v / 1000000 + "M") + }; + }); + + // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled. + if (ticks.length < 4) { + ticks[ticks.length-1].label = Math.round( + ( ticks[ticks.length-1].angle - d.startAngle ) / k / 1000000 + ) + "M"; + } + + return ticks; + }; + + var ticks = this.parent_elt.append("g") + .selectAll("g") + .data(this.chroms_layout) + .enter().append("g") + .selectAll("g") + .data(chromArcTicks) + .enter().append("g") + .attr("transform", function(d) { + return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + + "translate(" + self.innerRadius + ",0)"; + }); + + ticks.append("line") + .attr("x1", 1) + .attr("y1", 0) + .attr("x2", 4) + .attr("y2", 0) + .style("stroke", "#000"); + + ticks.append("text") + .attr("x", 4) + .attr("dy", ".35em") + .attr("text-anchor", function(d) { + return d.angle > Math.PI ? "end" : null; + }) + .attr("transform", function(d) { + return d.angle > Math.PI ? "rotate(180)translate(-16)" : null; + }) + .text(function(d) { return d.label; }); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in getting dataset id in 63f3b08
by Bitbucket 31 Oct '12

31 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8526b10ca125/ changeset: 8526b10ca125 user: jgoecks date: 2012-10-31 20:58:28 summary: Fix bug in getting dataset id in 63f3b08 affected #: 1 file diff -r 4ceab232dc02a5a99eca0b24c0038c490d49a392 -r 8526b10ca125a99de4d944e776e647c1598ffd06 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -249,7 +249,7 @@ # DEPRECATION: We still support unencoded ids for backward compatibility try: # encoded id? - dataset_id = trans.security.decode_id + dataset_id = trans.security.decode_id( dataset_id ) except ( AttributeError, TypeError ), err: # unencoded id Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 30 Oct '12

30 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8d3caff4bd0f/ changeset: 8d3caff4bd0f user: carlfeberhard date: 2012-10-30 21:53:10 summary: api/histories.show: add 'nice_size', 'annotation', 'state_ids' (map of possible hda states : lists of hda ids in those states ), reorder history state from child hda states (running/queued higher priority than error), return error string; affected #: 1 file diff -r 7b807f69906eff1ea1fa3ea367b299c628736d71 -r 8d3caff4bd0fc2e76bfdf47adc27930c538a9c1f lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -10,6 +10,10 @@ import galaxy.datatypes from galaxy.util.bunch import Bunch +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + log = logging.getLogger( __name__ ) class HistoriesController( BaseAPIController, UsesHistoryMixin ): @@ -31,12 +35,14 @@ item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append( item ) + elif trans.galaxy_session.current_history: #No user, this must be session authentication with an anonymous user. history = trans.galaxy_session.current_history item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) rval.append(item) + except Exception, e: rval = "Error in history API" log.error( rval + ": %s" % str(e) ) @@ -55,52 +61,90 @@ params = util.Params( kwd ) deleted = util.string_as_bool( deleted ) - def traverse( datasets ): - rval = {} - states = trans.app.model.Dataset.states + states = trans.app.model.Dataset.states + + def get_dataset_state_summaries( datasets ): + # cycles through the history's datasets, building counts and id lists for each possible ds state + state_counts = {} + state_ids = {} + + # init counts, ids for each state for key, state in states.items(): - rval[state] = 0 + state_counts[state] = 0 + state_ids[state] = [] + + # cycle through datasets saving each ds' state for dataset in datasets: - item = dataset.get_api_value( view='element' ) - if not item['deleted']: - rval[item['state']] = rval[item['state']] + 1 - return rval + dataset_dict = dataset.get_api_value( view='element' ) + item_state = dataset_dict[ 'state' ] + + if not dataset_dict['deleted']: + state_counts[ item_state ] = state_counts[ item_state ] + 1 + state_ids[ item_state ].append( trans.security.encode_id( dataset_dict[ 'id' ] ) ) + + return ( state_counts, state_ids ) + + # try to load the history, by most_recently_used or the given id try: if history_id == "most_recently_used": - if trans.user and len(trans.user.galaxy_sessions) > 0: + if trans.user and len( trans.user.galaxy_sessions ) > 0: # Most recent active history for user sessions, not deleted history = trans.user.galaxy_sessions[0].histories[-1].history else: - history = None + return None else: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) - except Exception, e: - return str( e ) - try: - item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) - num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] ) - states = trans.app.model.Dataset.states + history = self.get_history( trans, history_id, check_ownership=False, + check_accessible=True, deleted=deleted ) + + history_data = history.get_api_value( view='element', value_mapper={'id':trans.security.encode_id} ) + history_data[ 'nice_size' ] = history.get_disk_size( nice_size=True ) + + #TODO: separate, move to annotation api, fill on the client + history_data[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, history ) + if not history_data[ 'annotation' ]: + history_data[ 'annotation' ] = '' + + # get the history state using the state summaries of it's datasets (default to ERROR) + num_sets = len([ hda.id for hda in history.datasets if not hda.deleted ]) state = states.ERROR + + ( state_counts, state_ids ) = get_dataset_state_summaries( history.datasets ) + if num_sets == 0: state = states.NEW + else: - summary = traverse(history.datasets) - if summary[states.ERROR] > 0 or summary[states.FAILED_METADATA] > 0: + + if( ( state_counts[ states.RUNNING ] > 0 ) + or ( state_counts[ states.SETTING_METADATA ] > 0 ) + or ( state_counts[ states.UPLOAD ] > 0 ) ): + state = states.RUNNING + + elif state_counts[ states.QUEUED ] > 0: + state = states.QUEUED + + elif( ( state_counts[ states.ERROR ] > 0 ) + or ( state_counts[ states.FAILED_METADATA ] > 0 ) ): state = states.ERROR - elif summary[states.RUNNING] > 0 or summary[states.SETTING_METADATA] > 0: - state = states.RUNNING - elif summary[states.QUEUED] > 0: - state = states.QUEUED - elif summary[states.OK] == num_sets: + + elif state_counts[ states.OK ] == num_sets: state = states.OK - item['contents_url'] = url_for( 'history_contents', history_id=history_id ) - item['state_details'] = summary - item['state'] = state + + history_data[ 'state' ] = state + + history_data[ 'state_details' ] = state_counts + history_data[ 'state_ids' ] = state_ids + + history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) + + except Exception, e: - item = "Error in history API at showing history detail" - log.error(item + ": %s" % str(e)) + msg = "Error in history API at showing history detail: %s" % ( str( e ) ) + log.error( msg, exc_info=True ) trans.response.status = 500 - return item + return msg + + return history_data @web.expose_api def create( self, trans, payload, **kwd ): https://bitbucket.org/galaxy/galaxy-central/changeset/4ceab232dc02/ changeset: 4ceab232dc02 user: carlfeberhard date: 2012-10-30 21:55:23 summary: api/history_contents: (1) index: if passed ids=<id|csv id list> in query string, provide full data (as history_contents.show) for each id listed (if no 'ids' - use previous summary behaviour), return error string; (2) show: return 'accessible', 'api_type' (consistent with summary style in index), 'display_types', 'display_apps', 'file_ext', 'hid', 'history_id', 'meta_files' (file types of associated files for generating download urls, eg. myBam.meta_files: [{ 'file_type' : 'bam_index' }]), 'visualizations' (list of visualization names appr. for this hda), 'peek' (data.peek as used in the history panel), return error string; affected #: 1 file diff -r 8d3caff4bd0fc2e76bfdf47adc27930c538a9c1f -r 4ceab232dc02a5a99eca0b24c0038c490d49a392 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -2,8 +2,17 @@ API operations on the contents of a history. """ import logging +import urllib +from gettext import gettext + from galaxy import web -from galaxy.web.base.controller import BaseAPIController, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin, UsesHistoryMixin +from galaxy.web.base.controller import UsesLibraryMixin, UsesLibraryMixinItems + +from galaxy.web.framework.helpers import to_unicode +from galaxy.datatypes.display_applications import util +from galaxy.datatypes.metadata import FileParameter import pkg_resources pkg_resources.require( "Routes" ) @@ -11,27 +20,39 @@ log = logging.getLogger( __name__ ) -class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems ): - +class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, + UsesLibraryMixin, UsesLibraryMixinItems ): @web.expose_api - def index( self, trans, history_id, **kwd ): + def index( self, trans, history_id, ids=None, **kwd ): """ GET /api/histories/{encoded_history_id}/contents Displays a collection (list) of history contents """ + rval = [] try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - except Exception, e: - return str( e ) - rval = [] - try: - for dataset in history.datasets: - api_type = "file" - encoded_id = trans.security.encode_id( dataset.id ) - rval.append( dict( id = encoded_id, - type = api_type, - name = dataset.name, - url = url_for( 'history_content', history_id=history_id, id=encoded_id, ) ) ) + + # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history + if not ids: + for dataset in history.datasets: + api_type = "file" + encoded_id = trans.security.encode_id( dataset.id ) + # build the summary + rval.append( dict( id = encoded_id, + type = api_type, + name = dataset.name, + url = url_for( 'history_content', history_id=history_id, id=encoded_id, ) ) ) + + # if ids, return _FULL_ data (as show) for each id passed + #NOTE: this might not be the best form (passing all info), + # but we(I?) need an hda collection with full data somewhere + else: + ids = ids.split( ',' ) + for id in ids: + hda = self.get_history_dataset_association( trans, history, id, + check_ownership=True, check_accessible=True, check_state=False ) + rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + except Exception, e: rval = "Error in history API at listing contents" log.error( rval + ": %s" % str(e) ) @@ -44,30 +65,21 @@ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} Displays information about a history content (dataset). """ - content_id = id + hda_dict = {} try: - # get the history just for the access checks - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=False ) - content = self.get_history_dataset_association( trans, history, content_id, check_ownership=True, check_accessible=True ) + history = self.get_history( trans, history_id, + check_ownership=True, check_accessible=True, deleted=False ) + hda = self.get_history_dataset_association( trans, history, id, + check_ownership=True, check_accessible=True ) + hda_dict = get_hda_dict( trans, history, hda, for_editing=True ) + except Exception, e: - return str( e ) - try: - item = content.get_api_value( view='element' ) - if trans.user_is_admin() or trans.app.config.expose_dataset_path: - item['file_name'] = content.file_name - if not item['deleted']: - # Problem: Method url_for cannot use the dataset controller - # Get the environment from DefaultWebTransaction and use default webapp mapper instead of webapp API mapper - url = routes.URLGenerator(trans.webapp.mapper, trans.environ) - # http://routes.groovie.org/generating.html - # url_for is being phased out, so new applications should use url - item['download_url'] = url(controller='dataset', action='display', dataset_id=trans.security.encode_id(content.id), to_ext=content.ext) - item = self.encode_all_ids( trans, item ) - except Exception, e: - item = "Error in history API at listing dataset" - log.error( item + ": %s" % str(e) ) + msg = "Error in history API at listing dataset: %s" % ( str(e) ) + log.error( msg, exc_info=True ) trans.response.status = 500 - return item + return msg + + return hda_dict @web.expose_api def create( self, trans, history_id, payload, **kwd ): @@ -99,3 +111,69 @@ trans.response.status = 403 return "Not implemented." + +# move these into model?? hell if I know...doesn't seem like the urls should go here +def get_hda_dict( trans, history, hda, for_editing ): + hda_dict = hda.get_api_value( view='element' ) + + hda_dict[ 'id' ] = trans.security.encode_id( hda.id ) + hda_dict[ 'history_id' ] = trans.security.encode_id( history.id ) + hda_dict[ 'hid' ] = hda.hid + + hda_dict[ 'file_ext' ] = hda.ext + if trans.user_is_admin() or trans.app.config.expose_dataset_path: + hda_dict[ 'file_name' ] = hda.file_name + + if not hda_dict[ 'deleted' ]: + # Problem: Method url_for cannot use the dataset controller + # Get the environment from DefaultWebTransaction + # and use default webapp mapper instead of webapp API mapper + web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) + # http://routes.groovie.org/generating.html + # url_for is being phased out, so new applications should use url + hda_dict[ 'download_url' ] = web_url_for( controller='dataset', action='display', + dataset_id=trans.security.encode_id( hda.id ), to_ext=hda.ext ) + + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) + hda_dict[ 'api_type' ] = "file" + + if not( hda.purged or hda.deleted or hda.dataset.purged ): + meta_files = [] + for meta_type in hda.metadata.spec.keys(): + if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): + meta_files.append( dict( file_type=meta_type ) ) + if meta_files: + hda_dict[ 'meta_files' ] = meta_files + + #hda_dict[ 'display_apps' ] = get_display_apps( trans, hda ) + hda_dict[ 'visualizations' ] = hda.get_visualizations() + hda_dict[ 'peek' ] = to_unicode( hda.display_peek() ) + + return hda_dict + +def get_display_apps( trans, hda ): + display_apps = [] + + def get_display_app_url( display_app_link, hda, trans ): + web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) + dataset_hash, user_hash = util.encode_dataset_user( trans, hda, None ) + return web_url_for( controller='/dataset', + action="display_application", + dataset_id=dataset_hash, + user_id=user_hash, + app_name=urllib.quote_plus( display_app_link.display_application.id ), + link_name=urllib.quote_plus( display_app_link.id ) ) + + + for display_app in hda.get_display_applications( trans ).itervalues(): + app_links = [] + for display_app_link in display_app.links.itervalues(): + app_links.append({ + 'target' : display_app_link.url.get( 'target_frame', '_blank' ), + 'href' : get_display_app_url( display_app_link, hda, trans ), + 'text' : gettext( display_app_link.name ) + }) + display_apps.append( dict( label=display_app.name, links=app_links ) ) + + return display_apps Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: galaxy/exceptions: add __str__ to MessageException; galaxy/model: add hda.purged to hda.get_api_value
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7b807f69906e/ changeset: 7b807f69906e user: carlfeberhard date: 2012-10-30 21:50:37 summary: galaxy/exceptions: add __str__ to MessageException; galaxy/model: add hda.purged to hda.get_api_value affected #: 2 files diff -r 63f3b0857be8dae339622b23aa8d10b1ff3f3757 -r 7b807f69906eff1ea1fa3ea367b299c628736d71 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -9,6 +9,8 @@ def __init__( self, err_msg, type="info" ): self.err_msg = err_msg self.type = type + def __str__( self ): + return self.err_msg class ItemDeletionException( MessageException ): pass diff -r 63f3b0857be8dae339622b23aa8d10b1ff3f3757 -r 7b807f69906eff1ea1fa3ea367b299c628736d71 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1484,6 +1484,7 @@ model_class = self.__class__.__name__, name = hda.name, deleted = hda.deleted, + purged = hda.purged, visible = hda.visible, state = hda.state, file_size = int( hda.get_size() ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: controller/UsesHistoryDatasetAssociation: get_dataset: allow encoded ids; get_dataset, get_history_dataset_association: add check_state param: check hda.state == 'UPLOADING' to allow api fetch on uploading files, (should be backwards compat with existing calls)
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63f3b0857be8/ changeset: 63f3b0857be8 user: carlfeberhard date: 2012-10-30 21:46:55 summary: controller/UsesHistoryDatasetAssociation: get_dataset: allow encoded ids; get_dataset, get_history_dataset_association: add check_state param: check hda.state == 'UPLOADING' to allow api fetch on uploading files, (should be backwards compat with existing calls) affected #: 1 file diff -r 2e70816299e40fecc4902adda54126bb00316588 -r 63f3b0857be8dae339622b23aa8d10b1ff3f3757 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -244,20 +244,22 @@ class UsesHistoryDatasetAssociationMixin: """ Mixin for controllers that use HistoryDatasetAssociation objects. """ - def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False ): + def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True ): """ Get an HDA object by id. """ # DEPRECATION: We still support unencoded ids for backward compatibility try: - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - if data is None: - raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + # encoded id? + dataset_id = trans.security.decode_id + + except ( AttributeError, TypeError ), err: + # unencoded id + dataset_id = int( dataset_id ) + + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) except: - try: - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) - except: - data = None - if not data: raise HTTPRequestRangeNotSatisfiable( "Invalid dataset id: %s." % str( dataset_id ) ) + if check_ownership: # Verify ownership. user = trans.get_user() @@ -265,26 +267,30 @@ error( "Must be logged in to manage Galaxy items" ) if data.history.user != user: error( "%s is not owned by current user" % data.__class__.__name__ ) + if check_accessible: current_user_roles = trans.get_current_user_roles() - if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - if data.state == trans.model.Dataset.states.UPLOAD: - return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) - else: + + if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): error( "You are not allowed to access this dataset" ) + + if check_state and data.state == trans.model.Dataset.states.UPLOAD: + return trans.show_error_message( "Please wait until this dataset finishes uploading " + + "before attempting to view it." ) return data - def get_history_dataset_association( self, trans, history, dataset_id, check_ownership=True, check_accessible=False ): + def get_history_dataset_association( self, trans, history, dataset_id, + check_ownership=True, check_accessible=False, check_state=False ): """Get a HistoryDatasetAssociation from the database by id, verifying ownership.""" self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible ) hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False ) if check_accessible: - if trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): - if hda.state == trans.model.Dataset.states.UPLOAD: + if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): + error( "You are not allowed to access this dataset" ) + + if check_state and hda.state == trans.model.Dataset.states.UPLOAD: error( "Please wait until this dataset finishes uploading before attempting to view it." ) - else: - error( "You are not allowed to access this dataset" ) return hda def get_data( self, dataset, preview=True ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 30 Oct '12

30 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e825b868a31f/ changeset: e825b868a31f user: carlfeberhard date: 2012-10-30 21:39:47 summary: history.js: add hda updater, pull model data from common api code (in initial mako render, and on fetch/update), set up url templates for history, hda models affected #: 8 files diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -7,101 +7,182 @@ TODO: currently, adding a dataset (via tool execute, etc.) creates a new dataset and refreshes the page + from mako template: + BUG: imported, shared history with unaccessible dataset errs in historycontents when getting history + (entire history is inaccessible) + BUG: anon user, broken updater (upload) + added check_state to UsesHistoryDatasetAssocMixin + BUG: anon user + BUG: historyItem, error'd ds show display, download? + + from loadFromAPI: + BUG: not showing previous annotations + + fixed: + BUG: history, broken intial hist state (running, updater, etc.) + ??: doesn't seem to happen anymore + BUG: collapse all should remove all expanded from storage + FIXED: hideAllItemBodies now resets storage.expandedItems + BUG: historyItem, shouldn't allow tag, annotate, peek on purged datasets + FIXED: ok state now shows only: info, rerun + BUG: history?, some ids aren't returning encoded... + FIXED:??? + BUG: history, showing deleted ds + FIXED + UGH: historyItems have to be decorated with history_ids (api/histories/:history_id/contents/:id) + FIXED by adding history_id to history_contents.show + BUG: history, if hist has err'd ds, hist has perm state 'error', updater on following ds's doesn't run + FIXED by reordering history state from ds' states here and histories + BUG: history, broken annotation on reload (can't get thru api (sets fine, tho)) + FIXED: get thru api for now + + to relational model? + HDACollection, meta_files, display_apps, etc. + + + break this file up + localize all + ?: render url templates on init or render? + ?: history, annotation won't accept unicode + quota mgr + show_deleted/hidden: + use storage + on/off ui + move histview fadein/out in render to app? + don't draw body until it's first expand event + + hierarchy: + dataset -> hda + history -> historyForEditing, historyForViewing + display_structured? + + btw: get an error'd ds by running fastqc on fastq (when you don't have it installed) meta: + css/html class/id 'item' -> hda + add classes, ids on empty divs + events (local/ui and otherwise) require.js convert function comments to jsDoc style, complete comments move inline styles into base.less watch the magic strings watch your globals - all: - add classes, ids on empty divs - incorporate relations? - events (local/ui and otherwise) - have info bodies prev. opened, redisplay on refresh - transfer history.mako js: - updater, etc. - create viz icon - trackster - scatterplot - phylo-viz - on ready: - delete function - check_transfer_status (running->ok) - quota meter update - - historyItemView: - poly HistoryItemView (and HistoryView?) on: for_editing, display_structured, trans.user - don't draw body until it's first unhide event - HIview state transitions (eg. upload -> ok), curr: build new, delete old, place new (in render) - move visualizations menu - include phyloviz - - History: - renaming broken - tags rendering broken (url?) - annotation (url?) - meta controls : collapse all, rename, annotate, etc. - - collection: - show_deleted, show_hidden (thru js - no refresh) - + features: + lineage + hide button + show permissions in info + show shared/sharing status on ds, history + maintain scroll position on refresh (storage?) + selection, multi-select (and actions common to selected (ugh)) + searching + sorting, re-shuffling ============================================================================= */ -//TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted -var HistoryItem = BaseModel.extend( LoggableMixin ).extend({ +var HistoryDatasetAssociation = BaseModel.extend( LoggableMixin ).extend({ // a single HDA model // uncomment this out see log messages //logger : console, defaults : { + // ---these are part of an HDA proper: + + // parent (containing) history + history_id : null, + // often used with tagging + model_class : 'HistoryDatasetAssociation', + // index within history (??) + hid : 0, + // ---whereas these are Dataset related/inherited + id : null, - name : '', - data_type : null, - file_size : 0, - genome_build : null, - metadata_data_lines : 0, - metadata_dbkey : null, - metadata_sequences : 0, + name : '', + // one of HistoryDatasetAssociation.STATES + state : '', + // sniffed datatype (sam, tabular, bed, etc.) + data_type : null, + // size in bytes + file_size : 0, + + // array of associated file types (eg. [ 'bam_index', ... ]) + meta_files : [], misc_blurb : '', - misc_info : '', - model_class : '', - state : '', + misc_info : '', + deleted : false, purged : false, + // aka. !hidden + visible : false, + // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset )) + accessible : false, - // clash with BaseModel here? - visible : true, - - for_editing : true, - // additional urls will be passed and added, if permissions allow their use - - bodyIsShown : false + // this needs to be removed (it is a function of the view type (e.g. HDAForEditingView)) + for_editing : true + }, + + // fetch location of this history in the api + url : function(){ + //TODO: get this via url router + return 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); }, + // (curr) only handles changing state of non-accessible hdas to STATES.NOT_VIEWABLE + //TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted initialize : function(){ this.log( this + '.initialize', this.attributes ); this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); - //TODO: accessible is set in alt_hist - // this state is not in trans.app.model.Dataset.states - set it here + //!! this state is not in trans.app.model.Dataset.states - set it here if( !this.get( 'accessible' ) ){ - this.set( 'state', HistoryItem.STATES.NOT_VIEWABLE ); + this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); } + + this.on( 'change', function( event, x, y, z ){ + this.log( this + ' has changed:', event, x, y, z ); + }); }, + isDeletedOrPurged : function(){ + return ( this.get( 'deleted' ) || this.get( 'purged' ) ); + }, + + // roughly can_edit from history_common.mako - not deleted or purged = editable isEditable : function(){ - // roughly can_edit from history_common.mako - not deleted or purged = editable return ( //this.get( 'for_editing' ) - //&& !( this.get( 'deleted' ) || this.get( 'purged' ) ) - !( this.get( 'deleted' ) || this.get( 'purged' ) ) + //&& !( this.get( 'deleted' ) || this.get( 'purged' ) )?? + !this.isDeletedOrPurged() ); }, + + // based on show_deleted, show_hidden (gen. from the container control), would this ds show in the list of ds's? + //TODO: too many visibles + isVisible : function( show_deleted, show_hidden ){ + var isVisible = true; + if( ( !show_deleted ) + && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){ + isVisible = false; + } + if( ( !show_hidden ) + && ( !this.get( 'visible' ) ) ){ + isVisible = false; + } + return isVisible; + }, + // 'final' states are states where no processing (for the ds) is left to do on the server + inFinalState : function(){ + return ( + ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.OK ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.FAILED_METADATA ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.EMPTY ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + ); + }, + + // convenience fn to match hda.has_data hasData : function(){ //TODO:?? is this equivalent to all possible hda.has_data calls? return ( this.get( 'file_size' ) > 0 ); @@ -112,13 +193,13 @@ if( this.get( 'name' ) ){ nameAndId += ':"' + this.get( 'name' ) + '"'; } - return 'HistoryItem(' + nameAndId + ')'; + return 'HistoryDatasetAssociation(' + nameAndId + ')'; } }); //------------------------------------------------------------------------------ -HistoryItem.STATES = { - NOT_VIEWABLE : 'not_viewable', // not in trans.app.model.Dataset.states +HistoryDatasetAssociation.STATES = { + NOT_VIEWABLE : 'noPermission', // not in trans.app.model.Dataset.states NEW : 'new', UPLOAD : 'upload', QUEUED : 'queued', @@ -131,34 +212,310 @@ FAILED_METADATA : 'failed_metadata' }; +//============================================================================== +var HDACollection = Backbone.Collection.extend( LoggableMixin ).extend({ + model : HistoryDatasetAssociation, + + logger : console, + + // return the ids of every hda in this collection + ids : function(){ + return this.map( function( item ){ return item.id; }); + }, + + // return an HDA collection containing every 'shown' hda based on show_deleted/hidden + getVisible : function( show_deleted, show_hidden ){ + return new HDACollection( + this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }) + ); + }, + + // get a map where <possible hda state> : [ <list of hda ids in that state> ] + getStateLists : function(){ + var stateLists = {}; + _.each( _.values( HistoryDatasetAssociation.STATES ), function( state ){ + stateLists[ state ] = []; + }); + //NOTE: will err on unknown state + this.each( function( item ){ + stateLists[ item.get( 'state' ) ].push( item.get( 'id' ) ); + }); + return stateLists; + }, + + // update (fetch -> render) the hdas with the ids given + update : function( ids ){ + this.log( this + 'update:', ids ); + + if( !( ids && ids.length ) ){ return; } + + var collection = this; + _.each( ids, function( id, index ){ + var historyItem = collection.get( id ); + historyItem.fetch(); + }); + }, + + toString : function(){ + return ( 'HDACollection(' + this.ids().join(',') + ')' ); + } +}); + //============================================================================== -var HistoryItemView = BaseView.extend( LoggableMixin ).extend({ - //??TODO: add alias in initialize this.hda = this.model? - // view for HistoryItem model above +var History = BaseModel.extend( LoggableMixin ).extend({ + //TODO: bind change events from items and collection to this (itemLengths, states) // uncomment this out see log messages //logger : console, + // values from api (may need more) + defaults : { + id : '', + name : '', + state : '', + + //TODO: wire these to items (or this) + show_deleted : false, + show_hidden : false, + + diskSize : 0, + deleted : false, + + tags : [], + annotation : null, + + //TODO: quota msg and message? how to get those over the api? + message : null, + quotaMsg : false + }, + + url : function(){ + // api location of history resource + //TODO: hardcoded + return 'api/histories/' + this.get( 'id' ); + }, + + initialize : function( initialSettings, initialHdas ){ + this.log( this + ".initialize:", initialSettings, initialHdas ); + + this.hdas = new HDACollection(); + + // if we've got hdas passed in the constructor, load them and set up updates if needed + if( initialHdas && initialHdas.length ){ + this.hdas.reset( initialHdas ); + this.checkForUpdates(); + } + + this.on( 'change', function( event, x, y, z ){ + this.log( this + ' has changed:', event, x, y, z ); + }); + }, + + // get data via the api (alternative to sending options,hdas to initialize) + loadFromAPI : function( historyId, callback ){ + var history = this; + + // fetch the history AND the user (mainly to see if they're logged in at this point) + history.attributes.id = historyId; + //TODO:?? really? fetch user here? + jQuery.when( jQuery.ajax( 'api/users/current' ), history.fetch() + + ).then( function( userResponse, historyResponse ){ + //console.warn( 'fetched user, history: ', userResponse, historyResponse ); + history.attributes.user = userResponse[0]; //? meh. + history.log( history ); + + }).then( function(){ + // ...then the hdas (using contents?ids=...) + jQuery.ajax( history.url() + '/contents?' + jQuery.param({ + ids : history.itemIdsFromStateIds().join( ',' ) + + // reset the collection to the hdas returned + })).success( function( hdas ){ + //console.warn( 'fetched hdas' ); + history.hdas.reset( hdas ); + history.checkForUpdates(); + callback(); + }); + }); + }, + + // reduce the state_ids map of hda id lists -> a single list of ids + //...ugh - seems roundabout; necessary because the history doesn't have a straightforward list of ids + // (and history_contents/index curr returns a summary only) + hdaIdsFromStateIds : function(){ + return _.reduce( _.values( this.get( 'state_ids' ) ), function( reduction, currIdList ){ + return reduction.concat( currIdList ); + }); + }, + + // get the history's state from it's cummulative ds states, delay + update if needed + checkForUpdates : function( datasets ){ + // get overall History state from collection, run updater if History has running/queued hdas + this.stateFromStateIds(); + if( ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) + || ( this.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + this.stateUpdater(); + } + return this; + }, + + // sets history state based on current hdas' states + // ported from api/histories.traverse (with placement of error state changed) + stateFromStateIds : function(){ + var stateIdLists = this.hdas.getStateLists(); + this.attributes.state_ids = stateIdLists; + + //TODO: make this more concise + if( ( stateIdLists.running.length > 0 ) + || ( stateIdLists.upload.length > 0 ) + || ( stateIdLists.setting_metadata.length > 0 ) ){ + this.set( 'state', HistoryDatasetAssociation.STATES.RUNNING ); + + } else if( stateIdLists.queued.length > 0 ){ + this.set( 'state', HistoryDatasetAssociation.STATES.QUEUED ); + + } else if( ( stateIdLists.error.length > 0 ) + || ( stateIdLists.failed_metadata.length > 0 ) ){ + this.set( 'state', HistoryDatasetAssociation.STATES.ERROR ); + + } else if( stateIdLists.ok.length === this.hdas.length ){ + this.set( 'state', HistoryDatasetAssociation.STATES.OK ); + + } else { + throw( this + '.stateFromStateDetails: unable to determine ' + + 'history state from hda states: ' + this.get( 'state_ids' ) ); + } + return this; + }, + + // update this history, find any hda's running/queued, update ONLY those that have changed states, + // set up to run this again in some interval of time + stateUpdater : function(){ + var history = this, + oldState = this.get( 'state' ), + // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state + oldStateIds = this.get( 'state_ids' ); + + // pull from the history api + //TODO: fetch? + jQuery.ajax( 'api/histories/' + this.get( 'id' ) + + ).success( function( response ){ + //this.log( 'historyApiRequest, response:', response ); + history.set( response ); + history.log( 'current history state:', history.get( 'state' ), '(was)', oldState ); + + // for each state, check for the difference between old dataset states and new + // the goal here is to check ONLY those datasets that have changed states (not all datasets) + var changedIds = []; + _.each( _.keys( response.state_ids ), function( state ){ + var diffIds = _.difference( response.state_ids[ state ], oldStateIds[ state ] ); + // aggregate those changed ids + changedIds = changedIds.concat( diffIds ); + }); + + // send the changed ids (if any) to dataset collection to have them fetch their own model changes + if( changedIds.length ){ + history.hdas.update( changedIds ); + } + + // set up to keep pulling if this history in run/queue state + //TODO: magic number here + if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + setTimeout( function(){ + history.stateUpdater(); + }, 4000 ); + } + + }).error( function( xhr, status, error ){ + if( console && console.warn ){ + console.warn( 'Error getting history updates from the server:', xhr, status, error ); + } + alert( 'Error getting history updates from the server.\n' + error ); + }); + }, + + toString : function(){ + var nameString = ( this.get( 'name' ) )? + ( ',' + this.get( 'name' ) ) : ( '' ); + return 'History(' + this.get( 'id' ) + nameString + ')'; + } +}); + +//============================================================================== +var HDAView = BaseView.extend( LoggableMixin ).extend({ + //??TODO: add alias in initialize this.hda = this.model? + // view for HistoryDatasetAssociation model above + + // uncomment this out see log messages + logger : console, + tagName : "div", className : "historyItemContainer", // ................................................................................ SET UP initialize : function( attributes ){ - this.log( this + '.initialize:', this, this.model ); - this.visible = attributes.visible; + this.log( this + '.initialize:', attributes ); + + // render urlTemplates (gen. provided by GalaxyPaths) to urls + if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } + this.urls = this.renderUrls( attributes.urlTemplates, this.model.toJSON() ); + + // whether the body of this hda is expanded (shown) + this.expanded = attributes.expanded || false; + + // re-render the entire view on any model change + this.model.bind( 'change', this.render, this ); }, + // urlTemplates is a map (or nested map) of underscore templates (currently, anyhoo) + // use the templates to create the apropo urls for each action this ds could use + renderUrls : function( urlTemplates, modelJson ){ + var hdaView = this, + urls = {}; + _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ + // object == nested templates: recurse + if( _.isObject( urlTemplateOrObj ) ){ + urls[ urlKey ] = hdaView.renderUrls( urlTemplateOrObj, modelJson ); + + // string == template: + } else { + // meta_down load is a special case (see renderMetaDownloadUrls) + //TODO: should be a better (gen.) way to handle this case + if( urlKey === 'meta_download' ){ + urls[ urlKey ] = hdaView.renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); + } else { + urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); + } + } + }); + return urls; + }, + + // there can be more than one meta_file to download, so return a list of url and file_type for each + renderMetaDownloadUrls : function( urlTemplate, modelJson ){ + return _.map( modelJson.meta_files, function( meta_file ){ + return { + url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), + file_type : meta_file.file_type + }; + }); + }, + // ................................................................................ RENDER MAIN - //??: this style builds an entire, new DOM tree - is that what we want?? render : function(){ - var id = this.model.get( 'id' ), - state = this.model.get( 'state' ); - this.clearReferences(); - + var view = this, + id = this.model.get( 'id' ), + state = this.model.get( 'state' ), + itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ); + + this._clearReferences(); this.$el.attr( 'id', 'historyItemContainer-' + id ); - var itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ) + itemWrapper .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) .addClass( 'historyItem-' + state ); @@ -167,33 +524,52 @@ this.body = $( this._render_body() ); itemWrapper.append( this.body ); + //TODO: move to own function: setUpBehaviours + // we can potentially skip this step and call popupmenu directly on the download button + make_popup_menus( itemWrapper ); + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); - // we can potentially skip this step and call popupmenu directly on the download button - make_popup_menus( itemWrapper ); - - //TODO: better transition/method than this... - this.$el.children().remove(); - return this.$el.append( itemWrapper ); + // transition... + this.$el.fadeOut( 'fast', function(){ + view.$el.children().remove(); + view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ + view.log( view + ' rendered:', view.$el ); + view.trigger( 'rendered' ); + }); + }); + return this; }, - clearReferences : function(){ - //??TODO: best way? + //NOTE: button renderers have the side effect of caching their IconButtonViews to this view + // clear out cached sub-views, dom refs, etc. from prev. render + _clearReferences : function(){ + //??TODO: we should reset these in the button logic checks (i.e. if not needed this.button = null; return null) //?? do we really need these - not so far + //TODO: at least move these to a map this.displayButton = null; this.editButton = null; this.deleteButton = null; this.errButton = null; + this.showParamsButton = null; + this.rerunButton = null; + this.visualizationsButton = null; + this.tagButton = null; + this.annotateButton = null; }, // ................................................................................ RENDER WARNINGS + // hda warnings including: is deleted, is purged, is hidden (including links to further actions (undelete, etc.)) _render_warnings : function(){ // jQ errs on building dom with whitespace - if there are no messages, trim -> '' - return $( jQuery.trim( HistoryItemView.templates.messages( this.model.toJSON() ) ) ); + return $( jQuery.trim( HDAView.templates.messages( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); }, // ................................................................................ RENDER TITLEBAR + // the part of an hda always shown (whether the body is expanded or not): title link, title buttons _render_titleBar : function(){ var titleBar = $( '<div class="historyItemTitleBar" style="overflow: hidden"></div>' ); titleBar.append( this._render_titleButtons() ); @@ -203,6 +579,8 @@ }, // ................................................................................ display, edit attr, delete + // icon-button group for the common, most easily accessed actions + //NOTE: these are generally displayed for almost every hda state (tho poss. disabled) _render_titleButtons : function(){ // render the display, edit attr and delete icon-buttons var buttonDiv = $( '<div class="historyItemButtons"></div>' ); @@ -212,31 +590,45 @@ return buttonDiv; }, - //TODO: ?? the three title buttons render for err'd datasets: is this normal? + // icon-button to display this hda in the galaxy main iframe _render_displayButton : function(){ - // don't show display while uploading - if( this.model.get( 'state' ) === HistoryItem.STATES.UPLOAD ){ return null; } + // don't show display if not in final state, error'd, or not accessible + if( ( !this.model.inFinalState() ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } + var displayBtnData = { + icon_class : 'display' + }; + // show a disabled display if the data's been purged - displayBtnData = ( this.model.get( 'purged' ) )?({ - title : 'Cannot display datasets removed from disk', - enabled : false, - icon_class : 'display' + if( this.model.get( 'purged' ) ){ + displayBtnData.enabled = false; + displayBtnData.title = 'Cannot display datasets removed from disk'; - // if not, render the display icon-button with href - }):({ - title : 'Display data in browser', - href : this.model.get( 'display_url' ), - target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( null ), - icon_class : 'display' - }); + } else { + displayBtnData.title = 'Display data in browser'; + displayBtnData.href = this.urls.display; + } + + if( this.model.get( 'for_editing' ) ){ + displayBtnData.target = 'galaxy_main'; + } + this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); return this.displayButton.render().$el; }, + // icon-button to edit the attributes (format, permissions, etc.) this hda _render_editButton : function(){ // don't show edit while uploading, or if editable - if( ( this.model.get( 'state' ) === HistoryItem.STATES.UPLOAD ) + if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) || ( !this.model.get( 'for_editing' ) ) ){ return null; } @@ -245,7 +637,7 @@ deleted = this.model.get( 'deleted' ), editBtnData = { title : 'Edit attributes', - href : this.model.get( 'edit_url' ), + href : this.urls.edit, target : 'galaxy_main', icon_class : 'edit' }; @@ -254,29 +646,33 @@ //TODO: if for_editing if( deleted || purged ){ editBtnData.enabled = false; - } - if( deleted ){ - editBtnData.title = 'Undelete dataset to edit attributes'; - } else if( purged ){ - editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; + if( purged ){ + editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; + } else if( deleted ){ + editBtnData.title = 'Undelete dataset to edit attributes'; + } } this.editButton = new IconButtonView({ model : new IconButton( editBtnData ) }); return this.editButton.render().$el; }, + // icon-button to delete this hda _render_deleteButton : function(){ - // don't show delete if not editable - if( !this.model.get( 'for_editing' ) ){ return null; } + // don't show delete if... + if( ( !this.model.get( 'for_editing' ) ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } var deleteBtnData = { title : 'Delete', - href : this.model.get( 'delete_url' ), + href : this.urls[ 'delete' ], id : 'historyItemDeleter-' + this.model.get( 'id' ), icon_class : 'delete' }; - if( ( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ) - && ( !this.model.get( 'delete_url' ) ) ){ + if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ deleteBtnData = { title : 'Dataset is already deleted', icon_class : 'delete', @@ -288,22 +684,27 @@ }, // ................................................................................ titleLink + // render the hid and hda.name as a link (that will expand the body) _render_titleLink : function(){ - return $( jQuery.trim( HistoryItemView.templates.titleLink( this.model.toJSON() ) ) ); + return $( jQuery.trim( HDAView.templates.titleLink( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); }, // ................................................................................ RENDER BODY + // render the data/metadata summary (format, size, misc info, etc.) _render_hdaSummary : function(){ - var modelData = this.model.toJSON(); + var modelData = _.extend( this.model.toJSON(), { urls: this.urls } ); // if there's no dbkey and it's editable : pass a flag to the template to render a link to editing in the '?' if( this.model.get( 'metadata_dbkey' ) === '?' && this.model.isEditable() ){ _.extend( modelData, { dbkey_unknown_and_editable : true }); } - return HistoryItemView.templates.hdaSummary( modelData ); + return HDAView.templates.hdaSummary( modelData ); }, // ................................................................................ primary actions + // render the icon-buttons gen. placed underneath the hda summary _render_primaryActionButtons : function( buttonRenderingFuncs ){ var primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ), view = this; @@ -313,73 +714,124 @@ return primaryActionButtons; }, + // icon-button/popupmenu to down the data (and/or the associated meta files (bai, etc.)) for this hda _render_downloadButton : function(){ // don't show anything if the data's been purged if( this.model.get( 'purged' ) ){ return null; } // return either: a single download icon-button (if there are no meta files) // or a popupmenu with links to download assoc. meta files (if there are meta files) - var downloadLinkHTML = HistoryItemView.templates.downloadLinks( this.model.toJSON() ); + var downloadLinkHTML = HDAView.templates.downloadLinks( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ); //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); return $( downloadLinkHTML ); }, - //NOTE: button renderers have the side effect of caching their IconButtonViews to this view + // icon-button to show the input and output (stdout/err) for the job that created this hda _render_errButton : function(){ - if( ( this.model.get( 'state' ) !== HistoryItem.STATES.ERROR ) + if( ( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ) || ( !this.model.get( 'for_editing' ) ) ){ return null; } this.errButton = new IconButtonView({ model : new IconButton({ title : 'View or report this error', - href : this.model.get( 'report_error_url' ), + href : this.urls.report_error, target : 'galaxy_main', icon_class : 'bug' })}); return this.errButton.render().$el; }, + // icon-button to show the input and output (stdout/err) for the job that created this hda _render_showParamsButton : function(){ // gen. safe to show in all cases this.showParamsButton = new IconButtonView({ model : new IconButton({ title : 'View details', - href : this.model.get( 'show_params_url' ), + href : this.urls.show_params, target : 'galaxy_main', icon_class : 'information' }) }); return this.showParamsButton.render().$el; }, + // icon-button to re run the job that created this hda _render_rerunButton : function(){ if( !this.model.get( 'for_editing' ) ){ return null; } this.rerunButton = new IconButtonView({ model : new IconButton({ title : 'Run this job again', - href : this.model.get( 'rerun_url' ), + href : this.urls.rerun, target : 'galaxy_main', icon_class : 'arrow-circle' }) }); return this.rerunButton.render().$el; }, - _render_tracksterButton : function(){ - var trackster_urls = this.model.get( 'trackster_urls' ); + // build an icon-button or popupmenu based on the number of applicable visualizations + // also map button/popup clicks to viz setup functions + _render_visualizationsButton : function(){ + var dbkey = this.model.get( 'dbkey' ), + visualizations = this.model.get( 'visualizations' ), + visualization_url = this.urls.visualization, + popup_menu_dict = {}, + params = { + dataset_id: this.model.get( 'id' ), + hda_ldda: 'hda' + }; + if( !( this.model.hasData() ) || !( this.model.get( 'for_editing' ) ) - || !( trackster_urls ) ){ return null; } + || !( visualizations && visualizations.length ) + || !( visualization_url ) ){ + //console.warn( 'NOT rendering visualization icon' ) + return null; + } - this.tracksterButton = new IconButtonView({ model : new IconButton({ - title : 'View in Trackster', + // render the icon from template + this.visualizationsButton = new IconButtonView({ model : new IconButton({ + title : 'Visualize', + href : visualization_url, icon_class : 'chart_curve' })}); - this.errButton.render(); //?? needed? - this.errButton.$el.addClass( 'trackster-add' ).attr({ - 'data-url' : trackster_urls[ 'data-url' ], - 'action-url': trackster_urls[ 'action-url' ], - 'new-url' : trackster_urls[ 'new-url' ] - }); - return this.errButton.$el; + var $icon = this.visualizationsButton.render().$el; + $icon.addClass( 'visualize-icon' ); // needed? + + //TODO: make this more concise + // map a function to each visualization in the icon's attributes + // create a popupmenu from that map + // Add dbkey to params if it exists. + if( dbkey ){ params.dbkey = dbkey; } + + function create_viz_action( visualization ) { + switch( visualization ){ + case 'trackster': + return create_trackster_action_fn( visualization_url, params, dbkey ); + case 'scatterplot': + return create_scatterplot_action_fn( visualization_url, params ); + default: + return function(){ + window.parent.location = visualization_url + '/' + visualization + '?' + $.param( params ); }; + } + } + + // No need for popup menu because there's a single visualization. + if ( visualizations.length === 1 ) { + $icon.attr( 'title', visualizations[0] ); + $icon.click( create_viz_action( visualizations[0] ) ); + + // >1: Populate menu dict with visualization fns, make the popupmenu + } else { + _.each( visualizations, function( visualization ) { + //TODO: move to utils + var titleCaseVisualization = visualization.charAt( 0 ).toUpperCase() + visualization.slice( 1 ); + popup_menu_dict[ titleCaseVisualization ] = create_viz_action( visualization ); + }); + make_popupmenu( $icon, popup_menu_dict ); + } + return $icon; }, // ................................................................................ secondary actions + // secondary actions: currently tagging and annotation (if user is allowed) _render_secondaryActionButtons : function( buttonRenderingFuncs ){ // move to the right (same level as primary) var secondaryActionButtons = $( '<div/>' ), @@ -394,68 +846,82 @@ return secondaryActionButtons; }, + // icon-button to load and display tagging html + //TODO: these should be a sub-MV _render_tagButton : function(){ if( !( this.model.hasData() ) || !( this.model.get( 'for_editing' ) ) - || ( !this.model.get( 'retag_url' ) ) ){ return null; } + || ( !this.urls.tags.get ) ){ return null; } this.tagButton = new IconButtonView({ model : new IconButton({ title : 'Edit dataset tags', target : 'galaxy_main', - href : this.model.get( 'retag_url' ), + href : this.urls.tags.get, icon_class : 'tags' })}); return this.tagButton.render().$el; }, + // icon-button to load and display annotation html + //TODO: these should be a sub-MV _render_annotateButton : function(){ if( !( this.model.hasData() ) || !( this.model.get( 'for_editing' ) ) - || ( !this.model.get( 'annotate_url' ) ) ){ return null; } + || ( !this.urls.annotation.get ) ){ return null; } this.annotateButton = new IconButtonView({ model : new IconButton({ title : 'Edit dataset annotation', target : 'galaxy_main', - href : this.model.get( 'annotate_url' ), icon_class : 'annotate' })}); return this.annotateButton.render().$el; }, // ................................................................................ other elements - _render_tagArea : function(){ - if( !this.model.get( 'retag_url' ) ){ return null; } - //TODO: move to mvc/tags.js - return $( HistoryItemView.templates.tagArea( this.model.toJSON() ) ); - }, - - _render_annotationArea : function(){ - if( !this.model.get( 'annotate_url' ) ){ return null; } - //TODO: move to mvc/annotations.js - return $( HistoryItemView.templates.annotationArea( this.model.toJSON() ) ); - }, - + // render links to external genome display applications (igb, gbrowse, etc.) + //TODO: not a fan of the style on these _render_displayApps : function(){ - // render links to external genome display applications (igb, gbrowse, etc.) if( !this.model.hasData() ){ return null; } var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ - //this.log( this + 'display_types:', this.model.get( 'display_types' ) ); + //this.log( this + 'display_types:', this.model.get( 'urls' ).display_types ); //TODO:?? does this ever get used? displayAppsDiv.append( - HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_types }) + HDAView.templates.displayApps({ displayApps : this.model.get( 'display_types' ) }) ); } if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ - //this.log( this + 'display_apps:', this.model.get( 'display_apps' ) ); + //this.log( this + 'display_apps:', this.model.get( 'urls' ).display_apps ); displayAppsDiv.append( - HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_apps }) + HDAView.templates.displayApps({ displayApps : this.model.get( 'display_apps' ) }) ); } return displayAppsDiv; }, + //TODO: into sub-MV + // render the area used to load tag display + _render_tagArea : function(){ + if( !this.urls.tags.set ){ return null; } + //TODO: move to mvc/tags.js + return $( HDAView.templates.tagArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + )); + }, + + //TODO: into sub-MV + // render the area used to load annotation display + _render_annotationArea : function(){ + if( !this.urls.annotation.get ){ return null; } + //TODO: move to mvc/annotations.js + return $( HDAView.templates.annotationArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + )); + }, + + // render the data peek + //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible _render_peek : function(){ if( !this.model.get( 'peek' ) ){ return null; } return $( '<div/>' ).append( @@ -468,6 +934,7 @@ // ................................................................................ state body renderers // _render_body fns for the various states + //TODO: only render these on expansion (or already expanded) _render_body_not_viewable : function( parent ){ //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right parent.append( $( '<div>You do not have permission to view dataset.</div>' ) ); @@ -532,7 +999,7 @@ _render_body_failed_metadata : function( parent ){ //TODO: the css for this box is broken (unlike the others) // add a message box about the failure at the top of the body... - parent.append( $( HistoryItemView.templates.failedMetadata( this.model.toJSON() ) ) ); + parent.append( $( HDAView.templates.failedMetadata( this.model.toJSON() ) ) ); //...then render the remaining body as STATES.OK (only diff between these states is the box above) this._render_body_ok( parent ); }, @@ -540,12 +1007,25 @@ _render_body_ok : function( parent ){ // most common state renderer and the most complicated parent.append( this._render_hdaSummary() ); + + // return shortened form if del'd + //TODO: is this correct? maybe only on purged + if( this.model.isDeletedOrPurged() ){ + parent.append( this._render_primaryActionButtons([ + this._render_downloadButton, + this._render_showParamsButton, + this._render_rerunButton + ])); + return; + } + //NOTE: change the order here parent.append( this._render_primaryActionButtons([ this._render_downloadButton, this._render_errButton, this._render_showParamsButton, - this._render_rerunButton + this._render_rerunButton, + this._render_visualizationsButton ])); parent.append( this._render_secondaryActionButtons([ this._render_tagButton, @@ -570,7 +1050,6 @@ _render_body : function(){ //this.log( this + '_render_body' ); - var state = this.model.get( 'state' ); //this.log( 'state:', state, 'for_editing', for_editing ); //TODO: incorrect id (encoded - use hid?) @@ -579,48 +1058,45 @@ .addClass( 'historyItemBody' ) .attr( 'style', 'display: block' ); - //TODO: not a fan of this - switch( state ){ - case HistoryItem.STATES.NOT_VIEWABLE : - this._render_body_not_viewable( body ); + //TODO: not a fan of this dispatch + switch( this.model.get( 'state' ) ){ + case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : + this._render_body_not_viewable( body ); break; - case HistoryItem.STATES.UPLOAD : - this._render_body_uploading( body ); + case HistoryDatasetAssociation.STATES.UPLOAD : + this._render_body_uploading( body ); break; - case HistoryItem.STATES.QUEUED : - this._render_body_queued( body ); + case HistoryDatasetAssociation.STATES.QUEUED : + this._render_body_queued( body ); break; - case HistoryItem.STATES.RUNNING : + case HistoryDatasetAssociation.STATES.RUNNING : this._render_body_running( body ); break; - case HistoryItem.STATES.ERROR : - this._render_body_error( body ); + case HistoryDatasetAssociation.STATES.ERROR : + this._render_body_error( body ); break; - case HistoryItem.STATES.DISCARDED : - this._render_body_discarded( body ); + case HistoryDatasetAssociation.STATES.DISCARDED : + this._render_body_discarded( body ); break; - case HistoryItem.STATES.SETTING_METADATA : - this._render_body_setting_metadata( body ); + case HistoryDatasetAssociation.STATES.SETTING_METADATA : + this._render_body_setting_metadata( body ); break; - case HistoryItem.STATES.EMPTY : - this._render_body_empty( body ); + case HistoryDatasetAssociation.STATES.EMPTY : + this._render_body_empty( body ); break; - case HistoryItem.STATES.FAILED_METADATA : - this._render_body_failed_metadata( body ); + case HistoryDatasetAssociation.STATES.FAILED_METADATA : + this._render_body_failed_metadata( body ); break; - case HistoryItem.STATES.OK : - this._render_body_ok( body ); + case HistoryDatasetAssociation.STATES.OK : + this._render_body_ok( body ); break; default: //??: no body? body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) ); } + body.append( '<div style="clear: both"></div>' ); - body.append( '<div style="clear: both"></div>' ); - if( this.model.get( 'bodyIsShown' ) === false ){ - body.hide(); - } - if( this.visible ){ + if( this.expanded ){ body.show(); } else { body.hide(); @@ -636,6 +1112,8 @@ }, // ................................................................................ STATE CHANGES / MANIPULATION + // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide + //TODO: into sub-MV loadAndDisplayTags : function( event ){ //BUG: broken with latest //TODO: this is a drop in from history.mako - should use MV as well @@ -649,7 +1127,7 @@ // Need to fill tag element. $.ajax({ //TODO: the html from this breaks a couple of times - url: this.model.get( 'ajax_get_tag_url' ), + url: this.urls.tags.get, error: function() { alert( "Tagging failed" ); }, success: function(tag_elt_html) { tagElt.html(tag_elt_html); @@ -661,7 +1139,6 @@ // Tag element is filled; show. tagArea.slideDown("fast"); } - } else { // Hide. tagArea.slideUp("fast"); @@ -669,20 +1146,21 @@ return false; }, + // find the annotation area and, if initial: (via ajax) load the html for displaying it; otherwise, unhide/hide + //TODO: into sub-MV loadAndDisplayAnnotation : function( event ){ - //BUG: broken with latest //TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayAnnotation', event ); var annotationArea = this.$el.find( '.annotation-area' ), annotationElem = annotationArea.find( '.annotation-elt' ), - setAnnotationUrl = this.model.get( 'ajax_set_annotation_url' ); + setAnnotationUrl = this.urls.annotation.set; // Show or hide annotation area; if showing annotation area and it's empty, fill it. if ( annotationArea.is( ":hidden" ) ){ if( !jQuery.trim( annotationElem.html() ) ){ // Need to fill annotation element. $.ajax({ - url: this.model.get( 'ajax_get_annotation_url' ), + url: this.urls.annotation.get, error: function(){ alert( "Annotations failed" ); }, success: function( htmlFromAjax ){ if( htmlFromAjax === "" ){ @@ -710,253 +1188,264 @@ return false; }, - toggleBodyVisibility : function( visible ){ + // expand/collapse body + //side effect: trigger event + toggleBodyVisibility : function( event, expanded ){ var $body = this.$el.find( '.historyItemBody' ); - if( visible === undefined ){ - $body.toggle(); - } else if( visible ){ - $body.show(); + expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); + //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); + + if( expanded ){ + $body.slideDown( 'fast' ); } else { - $body.hide(); + $body.slideUp( 'fast' ); } - this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), $body.is( ':visible' ) ); + this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), expanded ); }, // ................................................................................ UTILTIY toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HistoryItemView(' + modelString + ')'; + return 'HDAView(' + modelString + ')'; } }); //------------------------------------------------------------------------------ -HistoryItemView.templates = { - warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], +HDAView.templates = { + warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], - messages : Handlebars.templates[ 'template-history-warning-messages' ], - titleLink : Handlebars.templates[ 'template-history-titleLink' ], - hdaSummary : Handlebars.templates[ 'template-history-hdaSummary' ], - downloadLinks : Handlebars.templates[ 'template-history-downloadLinks' ], - failedMetadata : Handlebars.templates[ 'template-history-failedMetaData' ], - tagArea : Handlebars.templates[ 'template-history-tagArea' ], - annotationArea : Handlebars.templates[ 'template-history-annotationArea' ], - displayApps : Handlebars.templates[ 'template-history-displayApps' ] + messages : Handlebars.templates[ 'template-history-warning-messages' ], + titleLink : Handlebars.templates[ 'template-history-titleLink' ], + hdaSummary : Handlebars.templates[ 'template-history-hdaSummary' ], + downloadLinks : Handlebars.templates[ 'template-history-downloadLinks' ], + failedMetadata : Handlebars.templates[ 'template-history-failedMetaData' ], + tagArea : Handlebars.templates[ 'template-history-tagArea' ], + annotationArea : Handlebars.templates[ 'template-history-annotationArea' ], + displayApps : Handlebars.templates[ 'template-history-displayApps' ] }; //============================================================================== -var HistoryCollection = Backbone.Collection.extend({ - model : HistoryItem, - - toString : function(){ - return ( 'HistoryCollection()' ); - } -}); +//TODO: these belong somewhere else + +//TODO: should be imported from scatterplot.js +//TODO: OR abstracted to 'load this in the galaxy_main frame' +function create_scatterplot_action_fn( url, params ){ + action = function() { + var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ), + final_url = url + '/scatterplot?' + $.param(params); + galaxy_main.attr( 'src', final_url ); + //TODO: this needs to go away + $( 'div.popmenu-wrapper' ).remove(); + return false; + }; + return action; +} + +// ----------------------------------------------------------------------------- +// Create trackster action function. +//TODO: should be imported from trackster.js +function create_trackster_action_fn(vis_url, dataset_params, dbkey) { + return function() { + var params = {}; + if (dbkey) { params.dbkey = dbkey; } + $.ajax({ + url: vis_url + '/list_tracks?f-' + $.param(params), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + success: function(table_html) { + var parent = window.parent; + + parent.show_modal("View Data in a New or Saved Visualization", "", { + "Cancel": function() { + parent.hide_modal(); + }, + "View in saved visualization": function() { + // Show new modal with saved visualizations. + parent.show_modal("Add Data to Saved Visualization", table_html, { + "Cancel": function() { + parent.hide_modal(); + }, + "Add to visualization": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + dataset_params.id = vis_id; + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + }); + } + }); + }, + "View in new visualization": function() { + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + } + }); + } + }); + return false; + }; +} //============================================================================== -var History = BaseModel.extend( LoggableMixin ).extend({ - //TODO: bind change events from items and collection to this (itemLengths, states) - - // uncomment this out see log messages - //logger : console, - - // values from api (may need more) - defaults : { - id : '', - name : '', - state : '', - //TODO:?? change these to a list of encoded ids? - state_details : { - discarded : 0, - empty : 0, - error : 0, - failed_metadata : 0, - ok : 0, - queued : 0, - running : 0, - setting_metadata: 0, - upload : 0 - }, - - // maybe security issues... - userIsAdmin : false, - userRoles : [], - //TODO: hardcoded - - //TODO: wire this to items - itemsLength : 0, - showDeleted : false, - showHidden : false, - - diskSize : 0, - deleted : false, - - // tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), - // tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") - tags : [], - annotation : null, - message : null, - quotaMsg : false, - - baseURL : null, - hideDeletedURL : null, - hideHiddenURL : null, - tagURL : null, - annotateURL : null - }, - - initialize : function( data, history_datasets ){ - //this.log( this + '.initialize', data, history_datasets ); - this.items = new HistoryCollection(); - }, - - toJSON : function(){ - // unfortunately, bb doesn't call 'get' to form the JSON meaning computed vals from get aren't used, so... - // a simple example of override and super call - var json = Backbone.Model.prototype.toJSON.call( this ); - json.itemsLength = this.items.length; - //this.log( this + '.json:', json ); - return json; - }, - - loadDatasetsAsHistoryItems : function( datasets ){ - //TODO: add via ajax - multiple datasets at once - // adds the given dataset/Item data to historyItems - // and updates this.state based on their states - //pre: datasets is a list of objs - //this.log( this + '.loadDatasets', datasets ); - var self = this, - selfID = this.get( 'id' ), - stateDetails = this.get( 'state_details' ); - - _.each( datasets, function( dataset, index ){ - //self.log( 'loading dataset: ', dataset, index ); - - // create an item sending along the history_id as well - var historyItem = new HistoryItem( - _.extend( dataset, { history_id: selfID } ) ); - //self.log( 'as History:', historyItem ); - self.items.add( historyItem ); - - // add item's state to running totals in stateDetails - var itemState = dataset.state; - stateDetails[ itemState ] += 1; - }); - - // get overall History state from totals - this.set( 'state_details', stateDetails ); - this._stateFromStateDetails(); - return this; - }, - - _stateFromStateDetails : function(){ - // sets this.state based on current historyItems' states - // ported from api/histories.traverse - //pre: state_details is current counts of dataset/item states - this.set( 'state', '' ); - var stateDetails = this.get( 'state_details' ); - - //TODO: make this more concise - if( ( stateDetails.error > 0 ) - || ( stateDetails.failed_metadata > 0 ) ){ - this.set( 'state', HistoryItem.STATES.ERROR ); - - } else if( ( stateDetails.running > 0 ) - || ( stateDetails.setting_metadata > 0 ) ){ - this.set( 'state', HistoryItem.STATES.RUNNING ); - - } else if( stateDetails.queued > 0 ){ - this.set( 'state', HistoryItem.STATES.QUEUED ); - - } else if( stateDetails.ok === this.items.length ){ - this.set( 'state', HistoryItem.STATES.OK ); - - } else { - throw( '_stateFromStateDetails: unable to determine ' - + 'history state from state details: ' + this.state_details ); - } - return this; - }, - - toString : function(){ - var nameString = ( this.get( 'name' ) )? - ( ',' + this.get( 'name' ) ) : ( '' ); - return 'History(' + this.get( 'id' ) + nameString + ')'; - } -}); - -//------------------------------------------------------------------------------ -// view for the HistoryCollection (as per current right hand panel) +// view for the HDACollection (as per current right hand panel) var HistoryView = BaseView.extend( LoggableMixin ).extend({ // uncomment this out see log messages - //logger : console, + logger : console, // direct attachment to existing element el : 'body.historyPage', - //TODO: add id? - initialize : function(){ - this.log( this + '.initialize:', this ); + // init with the model, urlTemplates, set up storage, bind HDACollection events + //NOTE: this will create or load PersistantStorage keyed under 'HistoryView.<id>' + //pre: you'll need to pass in the urlTemplates (urlTemplates : { history : {...}, hda : {...} }) + initialize : function( attributes ){ + this.log( this + '.initialize:', attributes ); + + // set up url templates + //TODO: prob. better to put this in class scope (as the handlebars templates), but... + // they're added to GalaxyPaths on page load (after this file is loaded) + if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } + if( !attributes.urlTemplates.history ){ throw( 'HDAView needs urlTemplates.history on initialize' ); } + if( !attributes.urlTemplates.hda ){ throw( 'HDAView needs urlTemplates.hda on initialize' ); } + this.urlTemplates = attributes.urlTemplates.history; + this.hdaUrlTemplates = attributes.urlTemplates.hda; + // data that needs to be persistant over page refreshes + // (note the key function which uses the history id as well) this.storage = new PersistantStorage( 'HistoryView.' + this.model.get( 'id' ), - { visibleItems : {} } + { expandedHdas : {} } ); - // set up the individual history items/datasets - this.initializeItems(); + //this.model.bind( 'change', this.render, this ); + + // bind events from the model's hda collection + this.model.hdas.bind( 'add', this.add, this ); + this.model.hdas.bind( 'reset', this.addAll, this ); + this.model.hdas.bind( 'all', this.all, this ); + + // set up instance vars + this.hdaViews = {}; + this.urls = {}; }, - initializeItems : function(){ - this.itemViews = {}; - var historyPanel = this; - - // set up a view for each item, init with model and listeners, cache to map ( model.id : view ) - this.model.items.each( function( item ){ - var itemId = item.get( 'id' ), - visible = historyPanel.storage.get( 'visibleItems' ).get( itemId ), - itemView = new HistoryItemView({ - model: item, - visible: visible + add : function( hda ){ + //console.debug( 'add.' + this, hda ); + //TODO + }, + + addAll : function(){ + //console.debug( 'addAll.' + this ); + // re render when all hdas are reset + this.render(); + }, + + all : function( event ){ + //console.debug( 'allItemEvents.' + this, event ); + //...for which to do the debuggings + }, + + // render the urls for this view using urlTemplates and the model data + renderUrls : function( modelJson ){ + var historyView = this; + + historyView.urls = {}; + _.each( this.urlTemplates, function( urlTemplate, urlKey ){ + historyView.urls[ urlKey ] = _.template( urlTemplate, modelJson ); + }); + return historyView.urls; + }, + + // render urls, historyView body, and hdas (if any are shown), fade out, swap, fade in, set up behaviours + render : function(){ + var historyView = this, + setUpQueueName = historyView.toString() + '.set-up', + newRender = $( '<div/>' ), + modelJson = this.model.toJSON(); + + // render the urls and add them to the model json + modelJson.urls = this.renderUrls( modelJson ); + + // render the main template, tooltips + //NOTE: this is done before the items, since item views should handle theirs themselves + newRender.append( HistoryView.templates.historyPanel( modelJson ) ); + historyView.$el.find( '.tooltip' ).tooltip(); + + // render hda views (if any) + if( !this.model.hdas.length + || !this.renderItems( newRender.find( '#' + this.model.get( 'id' ) + '-datasets' ) ) ){ + // if history is empty or no hdas would be rendered, show the empty message + newRender.find( '#emptyHistoryMessage' ).show(); + } + + // fade out existing, swap with the new, fade in, set up behaviours + $( historyView ).queue( setUpQueueName, function( next ){ + historyView.$el.fadeOut( 'fast', function(){ next(); }); + }); + $( historyView ).queue( setUpQueueName, function( next ){ + // swap over from temp div newRender + historyView.$el.html( '' ); + historyView.$el.append( newRender.children() ); + + historyView.$el.fadeIn( 'fast', function(){ next(); }); + }); + $( historyView ).queue( setUpQueueName, function( next ){ + this.log( historyView + ' rendered:', historyView.$el ); + + //TODO: ideally, these would be set up before the fade in (can't because of async save text) + historyView.setUpBehaviours(); + historyView.trigger( 'rendered' ); + next(); + }); + $( historyView ).dequeue( setUpQueueName ); + return this; + }, + + // set up a view for each item to be shown, init with model and listeners, cache to map ( model.id : view ) + renderItems : function( $whereTo ){ + this.hdaViews = {}; + var historyView = this, + show_deleted = this.model.get( 'show_deleted' ), + show_hidden = this.model.get( 'show_hidden' ), + visibleHdas = this.model.hdas.getVisible( show_deleted, show_hidden ); + + // only render the shown hdas + visibleHdas.each( function( hda ){ + var hdaId = hda.get( 'id' ), + expanded = historyView.storage.get( 'expandedHdas' ).get( hdaId ); + historyView.hdaViews[ hdaId ] = new HDAView({ + model : hda, + expanded : expanded, + urlTemplates : historyView.hdaUrlTemplates }); - historyPanel.setUpItemListeners( itemView ); - historyPanel.itemViews[ itemId ] = itemView; + historyView.setUpHdaListeners( historyView.hdaViews[ hdaId ] ); + // render it (NOTE: reverse order, newest on top (prepend)) + //TODO: by default send a reverse order list (although this may be more efficient - it's more confusing) + $whereTo.prepend( historyView.hdaViews[ hdaId ].render().$el ); + }); + return visibleHdas.length; + }, + + // set up HistoryView->HDAView listeners + setUpHdaListeners : function( hdaView ){ + var history = this; + + // use storage to maintain a list of hdas whose bodies are expanded + hdaView.bind( 'toggleBodyVisibility', function( id, visible ){ + if( visible ){ + history.storage.get( 'expandedHdas' ).set( id, true ); + } else { + history.storage.get( 'expandedHdas' ).deleteKey( id ); + } }); }, - setUpItemListeners : function( itemView ){ - var HistoryPanel = this; - - // use storage to maintain a list of items whose bodies are visible - itemView.bind( 'toggleBodyVisibility', function( id, visible ){ - if( visible ){ - HistoryPanel.storage.get( 'visibleItems' ).set( id, true ); - } else { - HistoryPanel.storage.get( 'visibleItems' ).deleteKey( id ); - } - }); - }, - - render : function(){ - this.$el.append( HistoryView.templates.historyPanel( this.model.toJSON() ) ); - this.log( this + ' rendered from template:', this.$el ); - - // set up aliases - this.itemsDiv = this.$el.find( '#' + this.model.get( 'id' ) + '-datasets' ); - - //TODO: set up widgets, tooltips, etc. - async_save_text( - "history-name-container", - "history-name", - this.model.get( 'renameURL' ), - "new_name", - 18 - ); - this.$el.find( '.tooltip' ).tooltip(); - - var historyAnnotationArea = this.$el.find( '#history-annotation-area' ); - $( '#history-annotate' ).click( function() { + // set up js/widget behaviours: tooltips, + //TODO: these should be either sub-MVs, or handled by events + setUpBehaviours : function(){ + // annotation slide down + var historyAnnotationArea = this.$( '#history-annotation-area' ); + this.$( '#history-annotate' ).click( function() { if ( historyAnnotationArea.is( ":hidden" ) ) { historyAnnotationArea.slideDown( "fast" ); } else { @@ -964,77 +1453,60 @@ } return false; }); - async_save_text( - "history-annotation-container", - "history-annotation", - this.model.get( 'annotateURL' ), - "new_annotation", - 18, - true, - 4 - ); - if( this.model.items.length ){ - // render to temp, move all at once, remove temp holder - var tempDiv = this._render_items(); - this.itemsDiv.append( tempDiv.children() ); - tempDiv.remove(); - } - }, + // title and annotation editable text + //NOTE: these use page scoped selectors - so these need to be in the page DOM before they're applicable + async_save_text( "history-name-container", "history-name", + this.urls.rename, "new_name", 18 ); - _render_items : function(){ - var div = $( '<div/>' ), - view = this; - //NOTE!: render in reverse (newest on top) via prepend (instead of append) - _.each( this.itemViews, function( itemView, viewId ){ - view.log( view + '.render_items:', viewId, itemView ); - div.prepend( itemView.render() ); - }); - return div; + async_save_text( "history-annotation-container", "history-annotation", + this.urls.annotate, "new_annotation", 18, true, 4 ); }, events : { - 'click #history-collapse-all' : 'hideAllItemBodies', + 'click #history-collapse-all' : 'hideAllHdaBodies', 'click #history-tag' : 'loadAndDisplayTags' }, - hideAllItemBodies : function(){ + // collapse all hda bodies + hideAllHdaBodies : function(){ _.each( this.itemViews, function( item ){ - item.toggleBodyVisibility( false ); + item.toggleBodyVisibility( null, false ); }); + this.storage.set( 'expandedHdas', {} ); }, + // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide + //TODO: into sub-MV loadAndDisplayTags : function( event ){ - //BUG: broken with latest - //TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayTags', event ); var tagArea = this.$el.find( '#history-tag-area' ), tagElt = tagArea.find( '.tag-elt' ); this.log( '\t tagArea', tagArea, ' tagElt', tagElt ); - // Show or hide tag area; if showing tag area and it's empty, fill it. + // Show or hide tag area; if showing tag area and it's empty, fill it if( tagArea.is( ":hidden" ) ){ if( !jQuery.trim( tagElt.html() ) ){ var view = this; // Need to fill tag element. $.ajax({ //TODO: the html from this breaks a couple of times - url: this.model.get( 'tagURL' ), + url: view.urls.tag, error: function() { alert( "Tagging failed" ); }, success: function(tag_elt_html) { - view.log( view + ' tag elt html (ajax)', tag_elt_html ); + //view.log( view + ' tag elt html (ajax)', tag_elt_html ); tagElt.html(tag_elt_html); tagElt.find(".tooltip").tooltip(); tagArea.slideDown("fast"); } }); } else { - // Tag element is filled; show. + // Tag element already filled: show tagArea.slideDown("fast"); } } else { - // Hide. + // Currently shown: Hide tagArea.slideUp("fast"); } return false; @@ -1049,12 +1521,10 @@ historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] }; - - //============================================================================== //return { // HistoryItem : HistoryItem, -// HitoryItemView : HistoryItemView, +// HDAView : HDAView, // HistoryCollection : HistoryCollection, // History : History, // HistoryView : HistoryView diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/templates/compiled/template-history-downloadLinks.js @@ -7,16 +7,18 @@ function program1(depth0,data) { var buffer = "", stack1, foundHelper; + buffer += "\n"; buffer += "\n<div popupmenu=\"dataset-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-popup\">\n <a class=\"action-button\" href=\""; - foundHelper = helpers.download_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\">Download Dataset</a>\n <a>Additional Files</a>\n "; - stack1 = depth0.meta_files; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>\n<div style=\"float:left;\" class=\"menubutton split popup\" id=\"dataset-"; @@ -24,36 +26,38 @@ if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-popup\">\n <a href=\""; - foundHelper = helpers.download_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n</div>\n"; return buffer;} function program2(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <a class=\"action-button\" href=\""; - foundHelper = helpers.meta_download_url; + foundHelper = helpers.url; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.meta_download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + else { stack1 = depth0.url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\">Download "; - foundHelper = helpers.meta_file_type; + foundHelper = helpers.file_type; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.meta_file_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + else { stack1 = depth0.file_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</a>\n "; return buffer;} function program4(depth0,data) { - var buffer = "", stack1, foundHelper; + var buffer = "", stack1; + buffer += "\n"; buffer += "\n<a href=\""; - foundHelper = helpers.download_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n"; return buffer;} - stack1 = depth0.meta_files; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { return stack1; } else { return ''; }}); diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/templates/compiled/template-history-failedMetaData.js +++ b/static/scripts/templates/compiled/template-history-failedMetaData.js @@ -6,11 +6,11 @@ function program1(depth0,data) { - var buffer = "", stack1, foundHelper; + var buffer = "", stack1; buffer += "\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href=\""; - foundHelper = helpers.edit_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.edit_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">set it manually or retry auto-detection</a>.\n"; return buffer;} diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/templates/compiled/template-history-hdaSummary.js +++ b/static/scripts/templates/compiled/template-history-hdaSummary.js @@ -8,9 +8,9 @@ var buffer = "", stack1, foundHelper; buffer += "\n <a href=\""; - foundHelper = helpers.edit_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.edit_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">"; foundHelper = helpers.metadata_dbkey; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -2,148 +2,130 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\"\n title=\"Click to rename history\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n "; + return buffer;} + +function program3(depth0,data) { + return "refresh";} -function program3(depth0,data) { +function program5(depth0,data) { return "collapse all";} -function program5(depth0,data) { +function program7(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n <a id=\"history-tag\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + buffer += "\n <a id=\"history-tag\" title=\""; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; return buffer;} -function program6(depth0,data) { +function program8(depth0,data) { return "Edit history tags";} -function program8(depth0,data) { +function program10(depth0,data) { return "Edit history annotation";} -function program10(depth0,data) { +function program12(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n<div class=\"historyLinks\">\n <a href=\""; - foundHelper = helpers.hideDeletedURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.hideDeletedURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += "\n <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_deleted; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\">"; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n</div>\n"; + buffer += "</a>\n "; return buffer;} -function program11(depth0,data) { +function program13(depth0,data) { return "hide deleted";} -function program13(depth0,data) { +function program15(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n<div class=\"historyLinks\">\n <a href=\""; - foundHelper = helpers.hideHiddenURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.hideHiddenURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += "\n <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_hidden; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\">"; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n</div>\n"; + buffer += "</a>\n "; return buffer;} -function program14(depth0,data) { +function program16(depth0,data) { return "hide hidden";} -function program16(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; - foundHelper = helpers.diskSize; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\" title=\"Click to rename history\">"; - foundHelper = helpers.name; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n \n "; - return buffer;} - function program18(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-size\">"; - foundHelper = helpers.diskSize; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n "; - return buffer;} - -function program20(depth0,data) { - - var buffer = "", stack1, foundHelper; buffer += "\n"; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} -function program21(depth0,data) { +function program19(depth0,data) { var stack1, foundHelper; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program22(depth0,data) { +function program20(depth0,data) { return "You are currently viewing a deleted history!";} -function program24(depth0,data) { +function program22(depth0,data) { var buffer = "", stack1; - buffer += "\n"; - buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n "; - buffer += "\n "; - buffer += "\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + buffer += "\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; stack1 = depth0.annotation; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(25, program25, data),fn:self.program(23, program23, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n </div>\n </div>\n</div>\n"; + buffer += "\n </div>\n </div>\n </div>\n "; return buffer;} -function program25(depth0,data) { +function program23(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; @@ -153,12 +135,12 @@ buffer += escapeExpression(stack1) + "\n "; return buffer;} -function program27(depth0,data) { +function program25(depth0,data) { return "\n <em>Describe or add notes to history</em>\n ";} -function program29(depth0,data) { +function program27(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n<div id=\"message-container\">\n <div class=\""; @@ -172,92 +154,82 @@ buffer += escapeExpression(stack1) + "\n </div><br />\n</div>\n"; return buffer;} -function program31(depth0,data) { +function program29(depth0,data) { return "\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n ";} -function program33(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n<div id=\""; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\">\n "; - buffer += "\n</div>\n\n"; - return buffer;} - -function program35(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\">\n"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n"; - return buffer;} -function program36(depth0,data) { +function program31(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start";} - buffer += "<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; + buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; + foundHelper = helpers.nice_size; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n "; + stack1 = depth0.user; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; - foundHelper = helpers.baseURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.baseURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; + buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n "; - stack1 = depth0.userRoles; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.base; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n<div class=\"clear\"></div>\n\n"; - buffer += "\n"; - stack1 = depth0.showDeleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); + buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n "; + stack1 = depth0.user; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - stack1 = depth0.showHidden; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); + buffer += "\n </div>\n</div>\n<div style=\"clear: both;\"></div>\n\n"; + buffer += "\n<div class=\"historyLinks\">\n "; + stack1 = depth0.show_deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; - stack1 = depth0.userRoles; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(18, program18, data),fn:self.program(16, program16, data)}); + buffer += "\n "; + stack1 = depth0.show_hidden; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n"; + buffer += "\n</div>\n\n"; stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; buffer += "\n"; - stack1 = depth0.userRoles; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); + buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n "; + stack1 = depth0.user; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; + buffer += "\n</div>\n\n"; stack1 = depth0.message; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(27, program27, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n<div id=\"quota-message-container\">\n "; stack1 = depth0.over_quota; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n\n"; - stack1 = depth0.itemsLength; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(35, program35, data),fn:self.program(33, program33, data)}); + buffer += "\n</div>\n\n<div id=\""; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/compiled/template-history-warning-messages.js --- a/static/scripts/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/templates/compiled/template-history-warning-messages.js @@ -6,46 +6,57 @@ function program1(depth0,data) { - var stack1, foundHelper; - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + var stack1; + stack1 = depth0.purged; + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} function program2(depth0,data) { - var buffer = "", stack1; - buffer += "\n This dataset has been deleted.\n "; - stack1 = depth0.undelete_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + var buffer = "", stack1, foundHelper; + buffer += "\n"; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} function program3(depth0,data) { + var buffer = "", stack1; + buffer += "\n This dataset has been deleted.\n "; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program4(depth0,data) { + var buffer = "", stack1, foundHelper; buffer += "\n Click <a href=\""; - foundHelper = helpers.undelete_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.undelete_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" class=\"historyItemUndelete\" id=\"historyItemUndeleter-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; - stack1 = depth0.purge_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; return buffer;} -function program4(depth0,data) { +function program5(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n or <a href=\""; - foundHelper = helpers.purge_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.purge_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" class=\"historyItemPurge\" id=\"historyItemPurger-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } @@ -53,45 +64,46 @@ buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to immediately remove it from disk\n "; return buffer;} -function program6(depth0,data) { +function program7(depth0,data) { var stack1, foundHelper; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program7(depth0,data) { +function program8(depth0,data) { return "\n This dataset has been deleted and removed from disk.\n";} -function program9(depth0,data) { +function program10(depth0,data) { var stack1, foundHelper; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program10(depth0,data) { +function program11(depth0,data) { var buffer = "", stack1; buffer += "\n This dataset has been hidden.\n "; - stack1 = depth0.unhide_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} -function program11(depth0,data) { +function program12(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n Click <a href=\""; - foundHelper = helpers.unhide_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.unhide_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; + stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" class=\"historyItemUnhide\" id=\"historyItemUnhider-"; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } @@ -104,11 +116,11 @@ if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.purged; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.visible; - stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } return buffer;}); })(); \ No newline at end of file diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -1,15 +1,17 @@ <script type="text/template" class="template-history" id="template-history-warning-messages"> -{{#if deleted}}{{#warningmessagesmall}} +{{#if deleted}}{{#unless purged}} +{{#warningmessagesmall}} This dataset has been deleted. - {{#if undelete_url}} - Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" + {{#if urls.undelete}} + Click <a href="{{ urls.undelete }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" target="galaxy_history">here</a> to undelete it - {{#if purge_url}} - or <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" + {{#if urls.purge}} + or <a href="{{ urls.purge }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" target="galaxy_history">here</a> to immediately remove it from disk {{/if}} {{/if}} -{{/warningmessagesmall}}{{/if}} +{{/warningmessagesmall}} +{{/unless}}{{/if}} {{#if purged}}{{#warningmessagesmall}} This dataset has been deleted and removed from disk. @@ -17,8 +19,8 @@ {{#unless visible}}{{#warningmessagesmall}} This dataset has been hidden. - {{#if unhide_url}} - Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" + {{#if urls.unhide}} + Click <a href="{{ urls.unhide }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" target="galaxy_history">here</a> to unhide it {{/if}} {{/warningmessagesmall}}{{/unless}} @@ -34,7 +36,7 @@ format: <span class="{{ data_type }}">{{ data_type }}</span>, database: {{#if dbkey_unknown_and_editable }} - <a href="{{ edit_url }}" target="galaxy_main">{{ metadata_dbkey }}</a> + <a href="{{ urls.edit }}" target="galaxy_main">{{ metadata_dbkey }}</a> {{else}} <span class="{{ metadata_dbkey }}">{{ metadata_dbkey }}</span> {{/if}} @@ -47,24 +49,26 @@ <script type="text/template" class="template-history" id="template-history-failedMetaData"> {{#warningmessagesmall}} An error occurred setting the metadata for this dataset. -You may be able to <a href="{{ edit_url }}" target="galaxy_main">set it manually or retry auto-detection</a>. +You may be able to <a href="{{ urls.edit }}" target="galaxy_main">set it manually or retry auto-detection</a>. {{/warningmessagesmall}} </script><script type="text/template" class="template-history" id="template-history-downloadLinks"> -{{#if meta_files}} -<div popupmenu="dataset-{{id}}-popup"> - <a class="action-button" href="{{download_url}}">Download Dataset</a> +{{#if urls.meta_download}} +{{! this will be built using a popupmenu }} +<div popupmenu="dataset-{{ id }}-popup"> + <a class="action-button" href="{{ urls.download }}">Download Dataset</a><a>Additional Files</a> - {{#each meta_files}} - <a class="action-button" href="{{meta_download_url}}">Download {{meta_file_type}}</a> + {{#each urls.meta_download}} + <a class="action-button" href="{{ url }}">Download {{ file_type }}</a> {{/each}} </div> -<div style="float:left;" class="menubutton split popup" id="dataset-{{id}}-popup"> - <a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a> +<div style="float:left;" class="menubutton split popup" id="dataset-{{ id }}-popup"> + <a href="{{ urls.download }}" title="Download" class="icon-button disk tooltip"></a></div> {{else}} -<a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a> +{{! otherwise a simple icon button }} +<a href="{{ urls.download }}" title="Download" class="icon-button disk tooltip"></a> {{/if}} </script> @@ -101,61 +105,54 @@ History panel/page - the main container for hdas (gen. on the left hand of the glx page) --><script type="text/template" class="template-history" id="template-history-historyPanel"> +{{! history name (if any) }} +<div id="history-name-area" class="historyLinks"> + <div id="history-name-container" style="position: relative;"> + {{! TODO: factor out conditional css }} + <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{nice_size}}</div> + {{#if user}} + <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" + title="Click to rename history">{{name}}</div> + {{/if}} + </div> +</div> +<div style="clear: both;"></div> + <div id="top-links" class="historyLinks"> - <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{baseURL}}"></a> + <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{urls.base}}"></a><a title='{{#local}}collapse all{{/local}}' id="history-collapse-all" class='icon-button toggle tooltip' href='javascript:void(0);'></a> - {{#if userRoles}} <div style="width: 40px; float: right; white-space: nowrap;"> + {{#if user}} <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a><a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a> + {{/if}} </div> +</div> +<div style="clear: both;"></div> + +{{! TODO: move to js with no reload - use each with historyLinks }} +<div class="historyLinks"> + {{#if show_deleted}} + <a href="{{urls.hide_deleted}}">{{#local}}hide deleted{{/local}}</a> + {{/if}} + {{#if show_hidden}} + <a href="{{urls.hide_hidden}}">{{#local}}hide hidden{{/local}}</a> {{/if}} </div> -<div class="clear"></div> - -{{! TODO: move to js with no reload - use each with historyLinks }} -{{#if showDeleted}} -<div class="historyLinks"> - <a href="{{hideDeletedURL}}">{{#local}}hide deleted{{/local}}</a> -</div> -{{/if}} - -{{#if showHidden}} -<div class="historyLinks"> - <a href="{{hideHiddenURL}}">{{#local}}hide hidden{{/local}}</a> -</div> -{{/if}} - -{{! history name (if any) }} -<div id="history-name-area" class="historyLinks"> - <div id="history-name-container" style="position: relative;"> - {{#if userRoles}} - {{! TODO: factor out conditional css }} - <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{diskSize}}</div> - <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">{{name}}</div> - - {{else}} - <div id="history-size">{{diskSize}}</div> - {{/if}} - </div> -</div> -<div style="clear: both;"></div> {{#if deleted}} {{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} {{/if}} {{! tags and annotations }} -{{#if userRoles}} {{! TODO: move inline styles out }} <div style="margin: 0px 5px 10px 5px"> + {{#if user}} <div id="history-tag-area" style="display: none"> - {{! load via js render_individual_tagging_element }} - {{! render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") }} <strong>Tags:</strong><div class="tag-elt"></div></div> @@ -172,8 +169,8 @@ </div></div></div> + {{/if}} </div> -{{/if}} {{#if message}} <div id="message-container"> @@ -192,14 +189,9 @@ {{/if}} </div> -{{#if itemsLength}} -<div id="{{id}}-datasets" class="history-datasets-list"> - {{! NOTE: HistoryItemViews will be appended here }} +<div id="{{id}}-datasets" class="history-datasets-list"></div> + +<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;"> + {{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} </div> - -{{else}}{{! no history items }} -<div class="infomessagesmall" id="emptyHistoryMessage"> -{{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} -</div> -{{/if}} </script> diff -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -1,5 +1,9 @@ <%inherit file="/base.mako"/> +<%def name="title()"> + ${_('Galaxy History')} +</%def> + ## --------------------------------------------------------------------------------------------------------------------- <%def name="create_localization_json( strings_to_localize )"> ## converts strings_to_localize (a list of strings) into a JSON dictionary of { string : localized string } @@ -49,369 +53,233 @@ %></%def> +## --------------------------------------------------------------------------------------------------------------------- +## all the possible history urls (primarily from web controllers at this point) +<%def name="get_history_url_templates()"> +<% + from urllib import unquote_plus + + history_class_name = history.__class__.__name__ + encoded_id_template = '<%= id %>' + + url_dict = { + # TODO:?? next 3 needed? + 'base' : h.url_for( controller="/history" ), + ##TODO: move these into the historyMV + 'hide_deleted' : h.url_for( controller="/history", show_deleted=False ), + 'hide_hidden' : h.url_for( controller="/history", show_hidden=False ), + + ##TODO: into their own MVs + 'rename' : h.url_for( controller="/history", action="rename_async", + id=encoded_id_template ), + 'tag' : h.url_for( controller='tag', action='get_tagging_elt_async', + item_class=history_class_name, item_id=encoded_id_template ), + 'annotate' : h.url_for( controller="/history", action="annotate_async", + id=encoded_id_template ) + } +%> +${ unquote_plus( h.to_json_string( url_dict ) ) } +</%def> ## --------------------------------------------------------------------------------------------------------------------- -<%def name="get_urls_for_hda( hda, encoded_data_id, for_editing )"> +## all the possible hda urls (primarily from web controllers at this point) - whether they should have them or not +##TODO: unify url_for btwn web, api +<%def name="get_hda_url_templates()"><% - from galaxy.datatypes.metadata import FileParameter - #print '\n', hda.name + from urllib import unquote_plus - data_dict = {} - def add_to_data( **kwargs ): - data_dict.update( kwargs ) - - #TODO??: better way to do urls (move into js galaxy_paths (decorate) - _not_ dataset specific) - deleted = hda.deleted - purged = hda.purged - - # ................................................................ link actions - #purged = purged or hda.dataset.purged //?? - # all of these urls are 'datasets/data_id/<action> - if not ( dataset_purged or purged ) and for_editing: - add_to_data( undelete_url=h.url_for( controller='dataset', action='undelete', dataset_id=encoded_data_id ) ) - # trans - if trans.app.config.allow_user_dataset_purge: - add_to_data( purge_url=h.url_for( controller='dataset', action='purge', dataset_id=encoded_data_id ) ) - - if not hda.visible: - add_to_data( unhide_url=h.url_for( controller='dataset', action='unhide', dataset_id=encoded_data_id ) ) - - - # ................................................................ title actions (display, edit, delete) - display_url = '' - if for_editing: - display_url = h.url_for( controller='dataset', action='display', dataset_id=encoded_data_id, preview=True, filename='' ) - else: - # Get URL for display only. - if hda.history.user and hda.history.user.username: - display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', - username=hda.history.user.username, slug=encoded_data_id, filename='' ) - else: - # HACK: revert to for_editing display URL when there is no user/username. This should only happen when - # there's no user/username because dataset is being displayed by history/view after error reported. - # There are no security concerns here because both dataset/display and dataset/display_by_username_and_slug - # check user permissions (to the same degree) before displaying. - display_url = h.url_for( controller='dataset', action='display', dataset_id=encoded_data_id, preview=True, filename='' ) - add_to_data( display_url=display_url ) - - # edit attr button - if for_editing: - if not( hda.deleted or hda.purged ): - edit_url = h.url_for( controller='dataset', action='edit', - dataset_id=encoded_data_id ) - add_to_data( edit_url=edit_url ) - - # delete button - if for_editing and not ( deleted or dataset_purged or purged ): - delete_url = h.url_for( controller='dataset', action='delete', - dataset_id=encoded_data_id, - show_deleted_on_refresh=show_deleted ) - add_to_data( delete_url=delete_url ) - - # ................................................................ primary actions (error, info, download) - # download links (hda and associated meta files) - if not hda.purged: - add_to_data( download_url=h.url_for( controller='/dataset', action='display', - dataset_id=encoded_data_id, to_ext=hda.ext ) ) - - meta_files = [] - for k in hda.metadata.spec.keys(): - if isinstance( hda.metadata.spec[ k ].param, FileParameter ): - file_type = k - download_url = h.url_for( controller='/dataset', action='get_metadata_file', - hda_id=encoded_data_id, metadata_name=file_type ) - meta_files.append( dict( meta_file_type=file_type, meta_download_url=download_url ) ) - - if meta_files: - add_to_data( meta_files=meta_files ) - - # error report - if for_editing: - #NOTE: no state == 'error' check - ##TODO: has to have an _UN_ encoded id - #report_error_url = h.url_for( controller='dataset', action='errors', id=encoded_data_id ) - report_error_url = h.url_for( controller='dataset', action='errors', id=hda.id ) - add_to_data( report_error_url=report_error_url ) - - # info/params - show_params_url = h.url_for( controller='dataset', action='show_params', dataset_id=encoded_data_id ) - add_to_data( show_params_url=show_params_url ) - - # rerun - if for_editing: - ##TODO: has to have an _UN_ encoded id - #rerun_url = h.url_for( controller='tool_runner', action='rerun', id=encoded_data_id ) - rerun_url = h.url_for( controller='tool_runner', action='rerun', id=hda.id ) - add_to_data( rerun_url=rerun_url ) - - # visualizations - if hda.ext in app.datatypes_registry.get_available_tracks(): - # do these need _localized_ dbkeys? - trackster_urls = {} - if hda.dbkey != '?': - data_url = h.url_for( controller='visualization', action='list_tracks', dbkey=hda.dbkey ) - data_url = hda.replace( 'dbkey', 'f-dbkey' ) - else: - data_url = h.url_for( controller='visualization', action='list_tracks' ) - trackster_urls[ 'hda-url' ] = data_url - trackster_urls[ 'action-url' ] = h.url_for( controller='visualization', action='trackster', dataset_id=encoded_data_id ) - trackster_urls[ 'new-url' ] = h.url_for( controller='visualization', action='trackster', dataset_id=encoded_data_id, default_dbkey=hda.dbkey ) - add_to_data( trackster_url=trackster_urls ) - - # display apps (igv, uscs) - display_types = [] - display_apps = [] - if( hda.state in [ 'ok', 'failed_metadata' ] - and hda.has_data() ): - #NOTE: these two data share structures - #TODO: this doesn't seem to get called with the hda I'm using. What would call this? How can I spoof it? - for display_type in hda.datatype.get_display_types(): - display_label = hda.datatype.get_display_label( display_type ) - target_frame, display_links = hda.datatype.get_display_links( hda, display_type, app, request.base ) - if display_links: - display_links = [] - for display_name, display_href in display_links: - display_type_link = dict( - target = target_frame, - href = display_href, - text = display_name - ) - display_links.append( display_type_link ) - - # append the link list to the main map using the display_label - display_types.append( dict( label=display_label, links=display_links ) ) + hda_class_name = 'HistoryDatasetAssociation' + encoded_id_template = '<%= id %>' + username_template = '<%= username %>' + hda_ext_template = '<%= file_ext %>' + meta_type_template = '<%= file_type %>' - for display_app in hda.get_display_applications( trans ).itervalues(): - app_links = [] - for display_app_link in display_app.links.itervalues(): - app_link = dict( - target = display_app_link.url.get( 'target_frame', '_blank' ), - href = display_app_link.get_display_url( hda, trans ), - text = _( display_app_link.name ) - ) - app_links.append( app_link ) - - display_apps.append( dict( label=display_app.name, links=app_links ) ) - - # attach the display types and apps (if any) to the hda obj - #if display_types: print 'display_types:', display_types - #if display_apps: print 'display_apps:', display_apps - add_to_data( display_types=display_types ) - add_to_data( display_apps=display_apps ) + url_dict = { + # ................................................................ warning message links + 'purge' : h.url_for( controller='dataset', action='purge', + dataset_id=encoded_id_template ), + #TODO: hide (via api) + 'unhide' : h.url_for( controller='dataset', action='unhide', + dataset_id=encoded_id_template ), + #TODO: via api + 'undelete' : h.url_for( controller='dataset', action='undelete', + dataset_id=encoded_id_template ), - # ................................................................ secondary actions (tagging, annotation) - if trans.user: - add_to_data( ajax_get_tag_url=( h.url_for( - controller='tag', action='get_tagging_elt_async', - item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) - add_to_data( retag_url=( h.url_for( - controller='tag', action='retag', - item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) - - add_to_data( annotate_url=( h.url_for( controller='dataset', action='annotate', id=encoded_data_id ) ) ) - add_to_data( ajax_get_annotation_url=( h.url_for( - controller='dataset', action='get_annotation_async', id=encoded_data_id ) ) ) - add_to_data( ajax_set_annotation_url=( h.url_for( - controller='/dataset', action='annotate_async', id=encoded_data_id ) ) ) - - return data_dict + # ................................................................ title actions (display, edit, delete), + 'display' : h.url_for( controller='dataset', action='display', + dataset_id=encoded_id_template, preview=True, filename='' ), + #'user_display_url' : h.url_for( controller='dataset', action='display_by_username_and_slug', + # username=username_template, slug=encoded_id_template, filename='' ), + 'edit' : h.url_for( controller='dataset', action='edit', + dataset_id=encoded_id_template ), + + #TODO: via api + #TODO: show deleted handled by history + 'delete' : h.url_for( controller='dataset', action='delete', + dataset_id=encoded_id_template, show_deleted_on_refresh=show_deleted ), + + # ................................................................ download links (and associated meta files), + 'download' : h.url_for( controller='/dataset', action='display', + dataset_id=encoded_id_template, to_ext=hda_ext_template ), + 'meta_download' : h.url_for( controller='/dataset', action='get_metadata_file', + hda_id=encoded_id_template, metadata_name=meta_type_template ), + + # ................................................................ primary actions (errors, params, rerun), + 'report_error' : h.url_for( controller='dataset', action='errors', + id=encoded_id_template ), + 'show_params' : h.url_for( controller='dataset', action='show_params', + dataset_id=encoded_id_template ), + 'rerun' : h.url_for( controller='tool_runner', action='rerun', + id=encoded_id_template ), + 'visualization' : h.url_for( controller='visualization' ), + + # ................................................................ secondary actions (tagging, annotation), + 'tags' : { + 'get' : h.url_for( controller='tag', action='get_tagging_elt_async', + item_class=hda_class_name, item_id=encoded_id_template ), + 'set' : h.url_for( controller='tag', action='retag', + item_class=hda_class_name, item_id=encoded_id_template ), + }, + 'annotation' : { + #'annotate_url' : h.url_for( controller='dataset', action='annotate', + # id=encoded_id_template ), # doesn't look like this is used (unless graceful degradation) + 'get' : h.url_for( controller='dataset', action='get_annotation_async', + id=encoded_id_template ), + 'set' : h.url_for( controller='/dataset', action='annotate_async', + id=encoded_id_template ), + }, + } +%> +${ unquote_plus( h.to_json_string( url_dict ) ) } +</%def> + +## ----------------------------------------------------------------------------- +## get the history, hda, user data from the api (as opposed to the web controllers/mako) + +## I'd rather do without these (esp. the get_hdas which hits the db twice) +## but we'd need a common map producer (something like get_api_value but more complete) +##TODO: api/web controllers should use common code, and this section should call that code +<%def name="get_history( id )"> +<% + return trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) %></%def> -<%def name="prep_hda( data, for_editing )"> +<%def name="get_current_user()"><% - from pprint import pformat - ## 'datasets' passed from root.history are HistoryDatasetAssociations - ## these datas _have_ a Dataset (data.dataset) - #ported mostly from history_common - #post: return dictionary form - #??: move out of templates? - #??: gather data from model? - - DATASET_STATE = trans.app.model.Dataset.states - # {'OK': 'ok', 'FAILED_METADATA': 'failed_metadata', 'UPLOAD': 'upload', - # 'DISCARDED': 'discarded', 'RUNNING': 'running', 'SETTING_METADATA': 'setting_metadata', - # 'ERROR': 'error', 'NEW': 'new', 'QUEUED': 'queued', 'EMPTY': 'empty'} - #TODO: move to Dataset.states? how often are these used? - STATES_INTERPRETED_AS_QUEUED = [ 'no state', '', None ] - - #TODO: clean up magic strings - #TODO: format to 120 - data_dict = data.get_api_value() - - # convert/re-format api values as needed - #TODO: use data_dict.update to add these (instead of localvars) - def add_to_data( **kwargs ): - data_dict.update( kwargs ) - - # trans - add_to_data( hid=data.hid ) - encoded_data_id = trans.security.encode_id( data.id ) - add_to_data( id=encoded_data_id ) - - # localize dbkey - data_dict[ 'metadata_dbkey' ] = _( data_dict[ 'metadata_dbkey' ] ) - - add_to_data( state=data.state ) - if data_state in STATES_INTERPRETED_AS_QUEUED: - #TODO: magic string - add_to_data( state=DATASET_STATE.QUEUED ) - - # trans - current_user_roles = trans.get_current_user_roles() - add_to_data( can_edit=( not ( data.deleted or data.purged ) ) ) - - # considered accessible if user can access or user isn't admin - # trans - accessible = trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ) - accessible = trans.user_is_admin() or accessible - add_to_data( accessible=accessible ) - - url_dict = get_urls_for_hda( data, encoded_data_id, for_editing ) - data_dict.update( url_dict ) - #print 'url_dict:', pformat( url_dict, indent=2 ) - #print 'data_dict:', pformat( data_dict, indent=2 ), "\n" - #print data_dict - - if data.peek != "no peek": - add_to_data( peek=( _( h.to_unicode( data.display_peek() ) ) ) ) - - return data_dict + if not trans.user: + return '{}' + return trans.webapp.api_controllers[ 'users' ].show( + trans, trans.security.encode_id( trans.user.id ) ) %></%def> -##TODO: remove after filling tags.js -<%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /> -<%def name="context_to_js()"> +<%def name="get_hdas( history_id, hdas )"><% - ##print 'context', context, dir( context ) - ##print 'context.kwargs', context.kwargs - ##print 'history:', history - - ##TODO: move to API - - for_editing = True - encoded_history_id = trans.security.encode_id( history.id ) - context_dict = { - 'history' : { - 'id' : encoded_history_id, - 'name' : history.name, - - 'status' : status, - 'showDeleted' : show_deleted, - 'showHidden' : show_hidden, - 'quotaMsg' : over_quota, - 'message' : message, ##'go outside' - - 'deleted' : history.deleted, - 'diskSize' : history.get_disk_size( nice_size=True ), - - ## maybe security issues... - 'userIsAdmin' : trans.user_is_admin(), - 'userRoles' : [ role.get_api_value() for role in trans.get_current_user_roles() ], - - ##tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), - ## tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") - 'tags' : [], - ##TODO: broken - of course - ##TODO: remove after filling tags.js - ##'tagHTML' : render_individual_tagging_element( - ## user=trans.get_user(), - ## tagged_item=history, - ## elt_context="history.mako", - ## use_toggle_link=False, - ## input_size="20"), - ##TODO:?? h.to_unicode( annotation ) | h - 'annotation' : h.to_unicode( annotation ), - - ##TODO: broken - 'baseURL' : h.url_for( controller="/history", show_deleted=show_deleted ), - 'hideDeletedURL' : h.url_for( controller="/history", show_deleted=False ), - 'hideHiddenURL' : h.url_for( controller="/history", show_hidden=False ), - 'renameURL' : h.url_for( controller="/history", action="rename_async", id=encoded_history_id ), - 'tagURL' : h.url_for( controller='tag', action='get_tagging_elt_async', - item_class=history.__class__.__name__, item_id=encoded_history_id ), - 'annotateURL' : h.url_for( controller="/history", action="annotate_async", id=encoded_history_id ) - }, - 'hdas' : [ prep_hda( hda, for_editing ) for hda in datasets ], - - # some of these may be unneeded when all is said and done... - 'hdaId' : hda_id, - 'forEditing' : for_editing, - } + if not hdas: + return '[]' + # rather just use the history.id (wo the datasets), but... + #BUG: one inaccessible dataset will error entire list + return trans.webapp.api_controllers[ 'history_contents' ].index( + trans, trans.security.encode_id( history_id ), + ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) ) %> -${ h.to_json_string( context_dict ) } </%def> +<%def name="print_visualizations( datasets )"> +<% + for dataset in datasets: + print trans.security.encode_id( dataset.id ) + print dataset.get_visualizations() + +%> +</%def> + +## ----------------------------------------------------------------------------- <%def name="javascripts()"> - ${parent.javascripts()} +${parent.javascripts()} + +${h.js( + "libs/jquery/jstorage", + "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", + "libs/json2", + "libs/backbone/backbone-relational", + "mvc/base-mvc", "mvc/ui" +)} + +${h.templates( + "helpers-common-templates", + "template-warningmessagesmall", - ${h.js( - "libs/jquery/jstorage", - "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", - "libs/json2", - "mvc/base-mvc", "mvc/ui" - )} + "template-history-warning-messages", + "template-history-titleLink", + "template-history-failedMetadata", + "template-history-hdaSummary", + "template-history-downloadLinks", + "template-history-tagArea", + "template-history-annotationArea", + "template-history-displayApps", + + "template-history-historyPanel" +)} - ${h.templates( - "helpers-common-templates", - "template-warningmessagesmall", +##TODO: fix: curr hasta be _after_ h.templates - move somehow +${h.js( + "mvc/history" + ##"mvc/tags", "mvc/annotations" +)} + +<script type="text/javascript"> +// set js localizable strings +GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); + +// add needed controller urls to GalaxyPaths +galaxy_paths.set( 'hda', ${get_hda_url_templates()} ); +galaxy_paths.set( 'history', ${get_history_url_templates()} ); + +$(function(){ + + // ostensibly, this is the App + if( console && console.debug ){ + //if( console.clear ){ console.clear(); } + console.debug( 'using backbone.js in history panel' ); + } + + // Navigate to a dataset. + console.debug( 'getting data' ); + var user = ${ get_current_user() }, + history = ${ get_history( history.id ) }, + hdas = ${ get_hdas( history.id, datasets ) }; + //console.debug( 'user:', user ); + //console.debug( 'history:', history ); + //console.debug( 'hdas:', hdas ); + + // i don't like this, but user authentication changes views/behaviour + history.user = user; + history.show_deleted = ${ 'true' if show_deleted else 'false' }; + history.show_hidden = ${ 'true' if show_hidden else 'false' }; - "template-history-warning-messages", - "template-history-titleLink", - "template-history-failedMetadata", - "template-history-hdaSummary", - "template-history-downloadLinks", - "template-history-tagArea", - "template-history-annotationArea", - "template-history-displayApps", - - "template-history-historyPanel" - )} + //console.debug( 'galaxy_paths:', galaxy_paths ); + var glx_history = new History( history, hdas ); + var glx_history_view = new HistoryView({ model: glx_history, urlTemplates: galaxy_paths.attributes }).render(); + + //var glx_history = new History().setPaths( galaxy_paths ), + // glx_history_view = new HistoryView({ model: glx_history }); + //console.warn( 'fetching' ); + //glx_history.loadFromAPI( pageData.history.id ); - ##TODO: fix: curr hasta be _after_ h.templates - move somehow - ${h.js( - "mvc/history" - ##"mvc/tags", "mvc/annotations" - )} - - <script type="text/javascript"> - GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); - // add needed controller urls to GalaxyPaths - galaxy_paths.set( 'dataset_path', "${h.url_for( controller='dataset' )}" ) - - // Init. on document load. - var pageData = ${context_to_js()}; - if( console && console.debug ){ - window.pageData = pageData; - - ##_.each( pageData.hdas, function( hda ){ - ## console.debug( hda ); - ##}); - } - - // on ready - USE_CURR_DATA = true; - $(function(){ - if( console && console.debug ){ console.debug( 'using backbone.js in history panel' ); } - - if ( window.USE_CURR_DATA ){ - // Navigate to a dataset. - if( pageData.hdaId ){ - self.location = "#" + pageData.hdaId; - } - var glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ), - glx_history_view = new HistoryView({ model: glx_history }); - glx_history_view.render(); - window.glx_history = glx_history; window.glx_history_view = glx_history_view; - - return; - - } else { - // sandbox - } - }); - </script> + if( console && console.debug ){ + window.user = top.user = user; + window._history = top._history = history; + window.hdas = top.hdas = hdas; + window.glx_history = top.glx_history = glx_history; + window.glx_history_view = top.glx_history_view = glx_history_view; + top.storage = jQuery.jStorage + } + + return; +}); +</script></%def> @@ -453,8 +321,4 @@ </noscript></%def> -<%def name="title()"> - ${_('Galaxy History')} -</%def> - <body class="historyPage"></body> https://bitbucket.org/galaxy/galaxy-central/changeset/2e70816299e4/ changeset: 2e70816299e4 user: carlfeberhard date: 2012-10-30 21:42:11 summary: pack scripts affected #: 6 files diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/mvc/history.js --- a/static/scripts/packed/mvc/history.js +++ b/static/scripts/packed/mvc/history.js @@ -1,1 +1,1 @@ -var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",this,this.model);this.visible=a.visible},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}if(this.visible){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b){var a=this.$el.find(".historyItemBody");if(b===undefined){a.toggle()}else{if(b){a.show()}else{a.hide()}}this.trigger("toggleBodyVisibility",this.model.get("id"),a.is(":visible"))},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HistoryItemView("+a+")"}});HistoryItemView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{visibleItems:{}});this.initializeItems()},initializeItems:function(){this.itemViews={};var a=this;this.model.items.each(function(c){var e=c.get("id"),d=a.storage.get("visibleItems").get(e),b=new HistoryItemView({model:c,visible:d});a.setUpItemListeners(b);a.itemViews[e]=b})},setUpItemListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("visibleItems").set(d,true)}else{a.storage.get("visibleItems").deleteKey(d)}})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");async_save_text("history-name-container","history-name",this.model.get("renameURL"),"new_name",18);this.$el.find(".tooltip").tooltip();var b=this.$el.find("#history-annotation-area");$("#history-annotate").click(function(){if(b.is(":hidden")){b.slideDown("fast")}else{b.slideUp("fast")}return false});async_save_text("history-annotation-container","history-annotation",this.model.get("annotateURL"),"new_annotation",18,true,4);if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(d,c){a.log(a+".render_items:",c,d);b.prepend(d.render())});return b},events:{"click #history-collapse-all":"hideAllItemBodies","click #history-tag":"loadAndDisplayTags"},hideAllItemBodies:function(){_.each(this.itemViews,function(a){a.toggleBodyVisibility(false)})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:this.model.get("tagURL"),error:function(){alert("Tagging failed")},success:function(e){a.log(a+" tag elt html (ajax)",e);b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"",state:"",data_type:null,file_size:0,meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:false,for_editing:true},url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change",function(b,a,d,c){this.log(this+" has changed:",b,a,d,c)})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isEditable:function(){return(!this.isDeletedOrPurged())},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inFinalState:function(){return((this.get("state")===HistoryDatasetAssociation.STATES.OK)||(this.get("state")===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(this.get("state")===HistoryDatasetAssociation.STATES.EMPTY)||(this.get("state")===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={NOT_VIEWABLE:"noPermission",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,logger:console,ids:function(){return this.map(function(a){return a.id})},getVisible:function(a,b){return new HDACollection(this.filter(function(c){return c.isVisible(a,b)}))},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return}var b=this;_.each(a,function(e,c){var d=b.get(e);d.fetch()})},toString:function(){return("HDACollection("+this.ids().join(",")+")")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",show_deleted:false,show_hidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}this.on("change",function(d,c,f,e){this.log(this+" has changed:",d,c,f,e)})},loadFromAPI:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){this.stateFromStateIds();if((this.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(this.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){this.stateUpdater()}return this},stateFromStateIds:function(){var a=this.hdas.getStateLists();this.attributes.state_ids=a;if((a.running.length>0)||(a.upload.length>0)||(a.setting_metadata.length>0)){this.set("state",HistoryDatasetAssociation.STATES.RUNNING)}else{if(a.queued.length>0){this.set("state",HistoryDatasetAssociation.STATES.QUEUED)}else{if((a.error.length>0)||(a.failed_metadata.length>0)){this.set("state",HistoryDatasetAssociation.STATES.ERROR)}else{if(a.ok.length===this.hdas.length){this.set("state",HistoryDatasetAssociation.STATES.OK)}else{throw (this+".stateFromStateDetails: unable to determine history state from hda states: "+this.get("state_ids"))}}}}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a);var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HDAView=BaseView.extend(LoggableMixin).extend({logger:console,tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,d=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+d);this._clearReferences();this.$el.attr("id","historyItemContainer-"+d);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);b.trigger("rendered")})});return this},_clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null;this.showParamsButton=null;this.rerunButton=null;this.visualizationsButton=null;this.tagButton=null;this.annotateButton=null},_render_warnings:function(){return $(jQuery.trim(HDAView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if((!this.model.inFinalState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={icon_class:"display"};if(this.model.get("purged")){a.enabled=false;a.title="Cannot display datasets removed from disk"}else{a.title="Display data in browser";a.href=this.urls.display}if(this.model.get("for_editing")){a.target="galaxy_main"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title="Cannot edit attributes of datasets removed from disk"}else{if(a){b.title="Undelete dataset to edit attributes"}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((!this.model.get("for_editing"))||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={title:"Delete",href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDAView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDAView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HDAView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a&&a.length)||!(f)){return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:"Visualize",href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[h]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.tags.get)){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.annotation.get)){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HDAView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b,a){var c=this.$el.find(".historyItemBody");a=(a===undefined)?(!c.is(":visible")):(a);if(a){c.slideDown("fast")}else{c.slideUp("fast")}this.trigger("toggleBodyVisibility",this.model.get("id"),a)},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(e){var f=window.parent;f.show_modal("View Data in a New or Saved Visualization","",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal("Add Data to Saved Visualization",e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}var HistoryView=BaseView.extend(LoggableMixin).extend({logger:console,el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{}});this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON();a.urls=this.renderUrls(a);c.append(HistoryView.templates.historyPanel(a));b.$el.find(".tooltip").tooltip();if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(e){b.$el.fadeOut("fast",function(){e()})});$(b).queue(d,function(e){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){e()})});$(b).queue(d,function(e){this.log(b+" rendered:",b.$el);b.setUpBehaviours();b.trigger("rendered");e()});$(b).dequeue(d);return this},renderItems:function(c){this.hdaViews={};var b=this,a=this.model.get("show_deleted"),e=this.model.get("show_hidden"),d=this.model.hdas.getVisible(a,e);d.each(function(h){var g=h.get("id"),f=b.storage.get("expandedHdas").get(g);b.hdaViews[g]=new HDAView({model:h,expanded:f,urlTemplates:b.hdaUrlTemplates});b.setUpHdaListeners(b.hdaViews[g]);c.prepend(b.hdaViews[g].render().$el)});return d.length},setUpHdaListeners:function(a){var b=this;a.bind("toggleBodyVisibility",function(d,c){if(c){b.storage.get("expandedHdas").set(d,true)}else{b.storage.get("expandedHdas").deleteKey(d)}})},setUpBehaviours:function(){var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},events:{"click #history-collapse-all":"hideAllHdaBodies","click #history-tag":"loadAndDisplayTags"},hideAllHdaBodies:function(){_.each(this.itemViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/packed/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/packed/templates/compiled/template-history-downloadLinks.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.meta_files;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.meta_download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_download_url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.meta_file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(s,r){var p="",q,o;p+='\n<a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n';return p}c=l.meta_files;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+="\n";p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';q=s.urls;q=q==null||q===false?q:q.download;q=typeof q===h?q():q;p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.urls;q=q==null||q===false?q:q.meta_download;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';q=s.urls;q=q==null||q===false?q:q.download;q=typeof q===h?q():q;p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.url;if(o){q=o.call(s,{hash:{}})}else{q=s.url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(r,q){var o="",p;o+="\n";o+='\n<a href="';p=r.urls;p=p==null||p===false?p:p.download;p=typeof p===h?p():p;o+=i(p)+'" title="Download" class="icon-button disk tooltip"></a>\n';return o}c=l.urls;c=c==null||c===false?c:c.meta_download;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/packed/templates/compiled/template-history-failedMetaData.js +++ b/static/scripts/packed/templates/compiled/template-history-failedMetaData.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(f,l,e,k,j){e=e||f.helpers;var c,h,g="function",i=this.escapeExpression,n=this,m=e.blockHelperMissing;function d(s,r){var p="",q,o;p+='\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href="';o=e.edit_url;if(o){q=o.call(s,{hash:{}})}else{q=s.edit_url;q=typeof q===g?q():q}p+=i(q)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return p}h=e.warningmessagesmall;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.warningmessagesmall;c=typeof c===g?c():c}if(!e.warningmessagesmall){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(f,l,e,k,j){e=e||f.helpers;var c,h,g="function",i=this.escapeExpression,n=this,m=e.blockHelperMissing;function d(r,q){var o="",p;o+='\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href="';p=r.urls;p=p==null||p===false?p:p.edit;p=typeof p===g?p():p;o+=i(p)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return o}h=e.warningmessagesmall;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.warningmessagesmall;c=typeof c===g?c():c}if(!e.warningmessagesmall){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/packed/templates/compiled/template-history-hdaSummary.js +++ b/static/scripts/packed/templates/compiled/template-history-hdaSummary.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <a href="';q=f.edit_url;if(q){s=q.call(u,{hash:{}})}else{s=u.edit_url;s=typeof s===h?s():s}r+=k(s)+'" 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";d=n.dbkey_unknown_and_editable;d=f["if"].call(n,d,{hash:{},inverse:p.program(3,c,l),fn:p.program(1,e,l)});if(d||d===0){j+=d}j+="\n</div>\n";d=n.misc_info;d=f["if"].call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}return j})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <a href="';s=u.urls;s=s==null||s===false?s:s.edit;s=typeof s===h?s():s;r+=k(s)+'" target="galaxy_main">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</a>\n ";return r}function c(u,t){var r="",s,q;r+='\n <span class="';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+'">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</span>\n ";return r}function o(u,t){var r="",s,q;r+='\n<div class="hda-info">';q=f.misc_info;if(q){s=q.call(u,{hash:{}})}else{s=u.misc_info;s=typeof s===h?s():s}r+=k(s)+"</div>\n";return r}j+='<div class="hda-summary">\n ';i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\n format: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\n database:\n ";d=n.dbkey_unknown_and_editable;d=f["if"].call(n,d,{hash:{},inverse:p.program(3,c,l),fn:p.program(1,e,l)});if(d||d===0){j+=d}j+="\n</div>\n";d=n.misc_info;d=f["if"].call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}return j})})(); \ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,C,A,s,J){A=A||k.helpers;var B="",o,n,y=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(L,K){return"refresh"}function t(L,K){return"collapse all"}function r(O,N){var L="",M,K;L+='\n <div style="width: 40px; float: right; white-space: nowrap;">\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a 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href="';K=A.hideHiddenURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideHiddenURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function F(L,K){return"hide hidden"}function E(O,N){var L="",M,K;L+="\n ";L+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+'</div>\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n \n ";return L}function D(O,N){var L="",M,K;L+='\n <div id="history-size">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function p(O,N){var L="",M,K;L+="\n";K=A.warningmessagesmall;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}else{M=O.warningmessagesmall;M=typeof M===f?M():M}if(!A.warningmessagesmall){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}if(M||M===0){L+=M}L+="\n";return L}function l(N,M){var L,K;K=A.local;if(K){L=K.call(N,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}else{L=N.local;L=typeof L===f?L():L}if(!A.local){L=c.call(N,L,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}if(L||L===0){return L}else{return""}}function j(L,K){return"You are currently viewing a deleted history!"}function i(N,M){var K="",L;K+="\n";K+='\n<div style="margin: 0px 5px 10px 5px">\n\n <div id="history-tag-area" style="display: none">\n ';K+="\n ";K+='\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';L=N.annotation;L=A["if"].call(N,L,{hash:{},inverse:y.program(27,g,M),fn:y.program(25,h,M)});if(L||L===0){K+=L}K+="\n </div>\n </div>\n </div>\n</div>\n";return K}function h(O,N){var L="",M,K;L+="\n ";K=A.annotation;if(K){M=K.call(O,{hash:{}})}else{M=O.annotation;M=typeof M===f?M():M}L+=e(M)+"\n ";return L}function g(L,K){return"\n <em>Describe or add notes to history</em>\n "}function d(O,N){var L="",M,K;L+='\n<div id="message-container">\n <div class="';K=A.status;if(K){M=K.call(O,{hash:{}})}else{M=O.status;M=typeof M===f?M():M}L+=e(M)+'message">\n ';K=A.message;if(K){M=K.call(O,{hash:{}})}else{M=O.message;M=typeof M===f?M():M}L+=e(M)+"\n </div><br />\n</div>\n";return L}function z(L,K){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n '}function x(O,N){var L="",M,K;L+='\n<div id="';K=A.id;if(K){M=K.call(O,{hash:{}})}else{M=O.id;M=typeof M===f?M():M}L+=e(M)+'-datasets" class="history-datasets-list">\n ';L+="\n</div>\n\n";return L}function w(O,N){var L="",M,K;L+='\n<div class="infomessagesmall" id="emptyHistoryMessage">\n';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}if(M||M===0){L+=M}L+="\n</div>\n";return L}function v(L,K){return"Your history is empty. Click 'Get Data' on the left pane to start"}B+='<div id="top-links" class="historyLinks">\n <a title="';n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}if(o||o===0){B+=o}B+='" class="icon-button arrow-circle tooltip" href="';n=A.baseURL;if(n){o=n.call(C,{hash:{}})}else{o=C.baseURL;o=typeof o===f?o():o}B+=e(o)+"\"></a>\n <a title='";n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}if(o||o===0){B+=o}B+="' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n ";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(5,r,J)});if(o||o===0){B+=o}B+='\n</div>\n<div class="clear"></div>\n\n';B+="\n";o=C.showDeleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(10,I,J)});if(o||o===0){B+=o}B+="\n\n";o=C.showHidden;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(13,G,J)});if(o||o===0){B+=o}B+="\n\n";B+='\n<div id="history-name-area" class="historyLinks">\n <div id="history-name-container" style="position: relative;">\n ';o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.program(18,D,J),fn:y.program(16,E,J)});if(o||o===0){B+=o}B+='\n </div> \n</div>\n<div style="clear: both;"></div>\n\n';o=C.deleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(20,p,J)});if(o||o===0){B+=o}B+="\n\n";B+="\n";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(24,i,J)});if(o||o===0){B+=o}B+="\n\n";o=C.message;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(29,d,J)});if(o||o===0){B+=o}B+='\n\n<div id="quota-message-container">\n ';o=C.over_quota;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(31,z,J)});if(o||o===0){B+=o}B+="\n</div>\n\n";o=C.itemsLength;o=A["if"].call(C,o,{hash:{},inverse:y.program(35,w,J),fn:y.program(33,x,J)});if(o||o===0){B+=o}return B})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,y,w,r,G){w=w||k.helpers;var x="",n,m,f="function",e=this.escapeExpression,u=this,c=w.blockHelperMissing;function t(L,K){var I="",J,H;I+='\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text"\n title="Click to rename history">';H=w.name;if(H){J=H.call(L,{hash:{}})}else{J=L.name;J=typeof J===f?J():J}I+=e(J)+"</div>\n ";return I}function s(I,H){return"refresh"}function q(I,H){return"collapse all"}function p(L,K){var I="",J,H;I+='\n <a id="history-tag" title="';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(8,l,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(8,l,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(10,F,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(10,F,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n ';return I}function l(I,H){return"Edit history tags"}function F(I,H){return"Edit history annotation"}function E(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_deleted;J=typeof J===f?J():J;I+=e(J)+'">';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(13,D,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(13,D,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function D(I,H){return"hide deleted"}function C(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_hidden;J=typeof J===f?J():J;I+=e(J)+'">';H=w.local;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(16,B,K)})}else{J=L.local;J=typeof J===f?J():J}if(!w.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(16,B,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function B(I,H){return"hide hidden"}function A(L,K){var I="",J,H;I+="\n";H=w.warningmessagesmall;if(H){J=H.call(L,{hash:{},inverse:u.noop,fn:u.program(19,z,K)})}else{J=L.warningmessagesmall;J=typeof J===f?J():J}if(!w.warningmessagesmall){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(19,z,K)})}if(J||J===0){I+=J}I+="\n";return I}function z(K,J){var I,H;H=w.local;if(H){I=H.call(K,{hash:{},inverse:u.noop,fn:u.program(20,o,J)})}else{I=K.local;I=typeof I===f?I():I}if(!w.local){I=c.call(K,I,{hash:{},inverse:u.noop,fn:u.program(20,o,J)})}if(I||I===0){return I}else{return""}}function o(I,H){return"You are currently viewing a deleted history!"}function j(K,J){var H="",I;H+='\n <div id="history-tag-area" style="display: none">\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';I=K.annotation;I=w["if"].call(K,I,{hash:{},inverse:u.program(25,h,J),fn:u.program(23,i,J)});if(I||I===0){H+=I}H+="\n </div>\n </div>\n </div>\n ";return H}function i(L,K){var I="",J,H;I+="\n ";H=w.annotation;if(H){J=H.call(L,{hash:{}})}else{J=L.annotation;J=typeof J===f?J():J}I+=e(J)+"\n ";return I}function h(I,H){return"\n <em>Describe or add notes to history</em>\n "}function g(L,K){var I="",J,H;I+='\n<div id="message-container">\n <div class="';H=w.status;if(H){J=H.call(L,{hash:{}})}else{J=L.status;J=typeof J===f?J():J}I+=e(J)+'message">\n ';H=w.message;if(H){J=H.call(L,{hash:{}})}else{J=L.message;J=typeof J===f?J():J}I+=e(J)+"\n </div><br />\n</div>\n";return I}function d(I,H){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. 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Click 'Get Data' on the left pane to start"}x+='\n<div id="history-name-area" class="historyLinks">\n <div id="history-name-container" style="position: relative;">\n ';x+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';m=w.nice_size;if(m){n=m.call(y,{hash:{}})}else{n=y.nice_size;n=typeof n===f?n():n}x+=e(n)+"</div>\n ";n=y.user;n=w["if"].call(y,n,{hash:{},inverse:u.noop,fn:u.program(1,t,G)});if(n||n===0){x+=n}x+='\n </div> \n</div>\n<div style="clear: both;"></div>\n\n<div id="top-links" class="historyLinks">\n <a title="';m=w.local;if(m){n=m.call(y,{hash:{},inverse:u.noop,fn:u.program(3,s,G)})}else{n=y.local;n=typeof n===f?n():n}if(!w.local){n=c.call(y,n,{hash:{},inverse:u.noop,fn:u.program(3,s,G)})}if(n||n===0){x+=n}x+='" class="icon-button arrow-circle tooltip" href="';n=y.urls;n=n==null||n===false?n:n.base;n=typeof n===f?n():n;x+=e(n)+"\"></a>\n <a title='";m=w.local;if(m){n=m.call(y,{hash:{},inverse:u.noop,fn:u.program(5,q,G)})}else{n=y.local;n=typeof n===f?n():n}if(!w.local){n=c.call(y,n,{hash:{},inverse:u.noop,fn:u.program(5,q,G)})}if(n||n===0){x+=n}x+="' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n <div style=\"width: 40px; 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\ No newline at end of file diff -r e825b868a31f4b2cdbeb951e73c34bc95eacd84c -r 2e70816299e40fecc4902adda54126bb00316588 static/scripts/packed/templates/compiled/template-history-warning-messages.js --- a/static/scripts/packed/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/packed/templates/compiled/template-history-warning-messages.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-warning-messages"]=b(function(g,s,q,k,v){q=q||g.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}if(x||x===0){return x}else{return""}}function n(z,y){var w="",x;w+="\n This dataset has been deleted.\n ";x=z.undelete_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(3,m,y)});if(x||x===0){w+=x}w+="\n";return w}function m(A,z){var x="",y,w;x+='\n Click <a href="';w=q.undelete_url;if(w){y=w.call(A,{hash:{}})}else{y=A.undelete_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUndelete" id="historyItemUndeleter-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to undelete it\n ';y=A.purge_url;y=q["if"].call(A,y,{hash:{},inverse:p.noop,fn:p.program(4,l,z)});if(y||y===0){x+=y}x+="\n ";return x}function l(A,z){var x="",y,w;x+='\n or <a href="';w=q.purge_url;if(w){y=w.call(A,{hash:{}})}else{y=A.purge_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemPurge" id="historyItemPurger-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return x}function j(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}if(x||x===0){return x}else{return""}}function i(x,w){return"\n This dataset has been deleted and removed from disk.\n"}function f(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}if(x||x===0){return x}else{return""}}function u(z,y){var w="",x;w+="\n This dataset has been hidden.\n ";x=z.unhide_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(11,t,y)});if(x||x===0){w+=x}w+="\n";return w}function t(A,z){var x="",y,w;x+='\n Click <a href="';w=q.unhide_url;if(w){y=w.call(A,{hash:{}})}else{y=A.unhide_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUnhide" id="historyItemUnhider-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to unhide it\n ';return x}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,v)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(6,j,v)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(9,f,v)});if(h||h===0){r+=h}return r})})(); 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\ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Data providers: (a) add option to report interchromosomal interactions and (b) pass kwargs to get_iterator method for filtering purposes.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0e2eb8ea274a/ changeset: 0e2eb8ea274a user: jgoecks date: 2012-10-30 20:15:11 summary: Data providers: (a) add option to report interchromosomal interactions and (b) pass kwargs to get_iterator method for filtering purposes. affected #: 2 files diff -r c0d8a9c916a50ef3f1fd7d67e987eba8f94e02a8 -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -150,7 +150,7 @@ """ raise Exception( "Unimplemented Function" ) - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end """ @@ -172,7 +172,7 @@ dataset_type, data """ start, end = int( low ), int( high ) - iterator = self.get_iterator( chrom, start, end ) + iterator = self.get_iterator( chrom, start, end, **kwargs ) return self.process_data( iterator, start_val, max_vals, **kwargs ) def get_genome_data( self, chroms_info, **kwargs ): @@ -338,7 +338,7 @@ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) if end >= (2<<29): end = (2<<29 - 1) # Tabix-enforced maximum @@ -387,7 +387,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): raise Exception( "Unimplemented Function" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -467,7 +467,7 @@ dataset_type = 'interval_index' - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): raise Exception( "Unimplemented Method" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -562,7 +562,7 @@ for large datasets. """ - def get_iterator( self, chrom=None, start=None, end=None ): + def get_iterator( self, chrom=None, start=None, end=None, **kwargs ): # Read first line in order to match chrom naming format. line = source.readline() dataset_chrom = line.split()[0] @@ -706,7 +706,7 @@ for large datasets. """ - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): # Read first line in order to match chrom naming format. line = source.readline() dataset_chrom = line.split()[0] @@ -864,7 +864,7 @@ new_bamfile.close() bamfile.close() - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end """ @@ -1174,7 +1174,7 @@ out.close() - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an array with values: (a) source file and (b) an iterator that provides data in the region chrom:start-end @@ -1233,7 +1233,7 @@ dataset_type = 'interval_index' - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end as well as a file offset. @@ -1341,7 +1341,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom, start, end, **kwargs ): raise "Unimplemented Method" def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -1487,7 +1487,7 @@ return 100000; class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ): - def get_iterator( self, chrom, start=0, end=sys.maxint ): + def get_iterator( self, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs ): """ """ # Modify start as needed to get earlier interactions with start region. @@ -1501,9 +1501,12 @@ c = feature[3] s2 = int( feature[4] ) e2 = int( feature[5] ) - #if ( s1 <= filter_end and e1 >= filter_start ) and ( s2 <= filter_end and e2 >= filter_start ) and ( max( s1, s2 ) - min( e1, e2 ) <= span * 2 ): + # Check for intrachromosal interactions. if ( ( s1 + s2 ) / 2 <= end ) and ( ( e1 + e2 ) / 2 >= start ) and ( c == chrom ): yield line + # Check for interchromosal interactions. + if interchromosomal and c != chrom: + yield line return filter( TabixDataProvider.get_iterator( self, chrom, filter_start, end ) ) # diff -r c0d8a9c916a50ef3f1fd7d67e987eba8f94e02a8 -r 0e2eb8ea274a1fedc2620f02adb6bbda81979f53 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -630,8 +630,10 @@ data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source=source ) - # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - rval = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + # HACK: pass in additional params which are used for only some types of data providers; + # level, cutoffs used for summary tree, and interchromosomal used for chromatin interactions. + rval = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0, + interchromosomal=True ) return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Tabular Display: left-align 'list' column type.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c0d8a9c916a5/ changeset: c0d8a9c916a5 user: dannon date: 2012-10-30 20:08:59 summary: Tabular Display: left-align 'list' column type. affected #: 1 file diff -r 172502ced921425b301725949bd8a82ff858bc48 -r c0d8a9c916a50ef3f1fd7d67e987eba8f94e02a8 templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -18,7 +18,7 @@ if (colspan !== undefined){ return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } - else if (COLUMN_TYPES[index] == 'str'){ + else if (COLUMN_TYPES[index] == 'str' || COLUMN_TYPES[index] == 'list'){ /* Left align all str columns, right align the rest */ return $('<td>').addClass('stringalign').text(cell_contents);; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: When migrating tools, if install_dependencies is True, but tool_dependency_dir is not set, do not attempt to install, but print informative error message.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/172502ced921/ changeset: 172502ced921 user: dan date: 2012-10-30 19:46:12 summary: When migrating tools, if install_dependencies is True, but tool_dependency_dir is not set, do not attempt to install, but print informative error message. affected #: 1 file diff -r 394c3bd89926919b3ff861d5bc3daa6c7d10fd12 -r 172502ced921425b301725949bd8a82ff858bc48 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -19,6 +19,10 @@ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config + # If install_dependencies is True, but tool_dependency_dir is not set, + # do not attempt to install, but print informative error message + if install_dependencies and app.config.tool_dependency_dir is None: + raise Exception( 'You are attempting to install tool dependencies, but do not have a value for "tool_dependency_dir" set in your ini file. Please set this to the path where you would like to install dependencies and rerun the migration script.' ) # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b) remove version information from jQuery UI file names; (c) add generic jQueryUI search+select combobox widget; (d) use combobox widget for choosing dbkey in Trackster visualizations. Also pack scripts.
by Bitbucket 30 Oct '12

30 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/394c3bd89926/ changeset: 394c3bd89926 user: jgoecks date: 2012-10-30 14:07:29 summary: UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b)= remove version information from jQuery UI file names; (c) add generic jQue= ryUI search+select combobox widget; (d) use combobox widget for choosing db= key in Trackster visualizations. Also pack scripts. affected #: 27 files diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/images/u= i-bg_glass_55_fbf9ee_1x400.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-bg_g= lass_55_fbf9ee_1x400.png has changed diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/images/u= i-icons_2e83ff_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icon= s_2e83ff_256x240.png has changed diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/jquery-u= i-1.8.23.custom.css --- a/static/june_2007_style/blue/jquery-ui/smoothness/jquery-ui-1.8.23.cus= tom.css +++ /dev/null @@ -1,363 +0,0 @@ -/*! - * jQuery UI CSS Framework 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - */ - -/* Layout helpers -----------------------------------*/ -.ui-helper-hidden { display: none; } -.ui-helper-hidden-accessible { position: absolute !important; clip: rect(1= px 1px 1px 1px); clip: rect(1px,1px,1px,1px); } -.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-heig= ht: 1.3; text-decoration: none; font-size: 100%; list-style: none; } -.ui-helper-clearfix:before, .ui-helper-clearfix:after { content: ""; displ= ay: table; } -.ui-helper-clearfix:after { clear: both; } -.ui-helper-clearfix { zoom: 1; } -.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: ab= solute; opacity: 0; filter:Alpha(Opacity=3D0); } - - -/* Interaction Cues -----------------------------------*/ -.ui-state-disabled { cursor: default !important; } - - -/* Icons -----------------------------------*/ - -/* states and images */ -.ui-icon { display: block; text-indent: -99999px; overflow: hidden; backgr= ound-repeat: no-repeat; } - - -/* Misc visuals -----------------------------------*/ - -/* Overlays */ -.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; hei= ght: 100%; } - - -/*! - * jQuery UI CSS Framework 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - * - * To view and modify this theme, visit http://jqueryui.com/themeroller/?f= fDefault=3DVerdana,Arial,sans-serif&fwDefault=3Dnormal&fsDefault=3D1.1em&co= rnerRadius=3D4px&bgColorHeader=3Dcccccc&bgTextureHeader=3D03_highlight_soft= .png&bgImgOpacityHeader=3D75&borderColorHeader=3Daaaaaa&fcHeader=3D222222&i= conColorHeader=3D222222&bgColorContent=3Dffffff&bgTextureContent=3D01_flat.= png&bgImgOpacityContent=3D75&borderColorContent=3Daaaaaa&fcContent=3D222222= &iconColorContent=3D222222&bgColorDefault=3De6e6e6&bgTextureDefault=3D02_gl= ass.png&bgImgOpacityDefault=3D75&borderColorDefault=3Dd3d3d3&fcDefault=3D55= 5555&iconColorDefault=3D888888&bgColorHover=3Ddadada&bgTextureHover=3D02_gl= ass.png&bgImgOpacityHover=3D75&borderColorHover=3D999999&fcHover=3D212121&i= conColorHover=3D454545&bgColorActive=3Dffffff&bgTextureActive=3D02_glass.pn= g&bgImgOpacityActive=3D65&borderColorActive=3Daaaaaa&fcActive=3D212121&icon= ColorActive=3D454545&bgColorHighlight=3Dfbf9ee&bgTextureHighlight=3D02_glas= s.png&bgImgOpacityHighlight=3D55&borderColorHighlight=3Dfcefa1&fcHighlight= =3D363636&iconColorHighlight=3D2e83ff&bgColorError=3Dfef1ec&bgTextureError= =3D02_glass.png&bgImgOpacityError=3D95&borderColorError=3Dcd0a0a&fcError=3D= cd0a0a&iconColorError=3Dcd0a0a&bgColorOverlay=3Daaaaaa&bgTextureOverlay=3D0= 1_flat.png&bgImgOpacityOverlay=3D0&opacityOverlay=3D30&bgColorShadow=3Daaaa= aa&bgTextureShadow=3D01_flat.png&bgImgOpacityShadow=3D0&opacityShadow=3D30&= thicknessShadow=3D8px&offsetTopShadow=3D-8px&offsetLeftShadow=3D-8px&corner= RadiusShadow=3D8px - */ - - -/* Component containers -----------------------------------*/ -.ui-widget { font-family: Verdana,Arial,sans-serif; font-size: 1.1em; } -.ui-widget .ui-widget { font-size: 1em; } -.ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget butto= n { font-family: Verdana,Arial,sans-serif; font-size: 1em; } -.ui-widget-content { border: 1px solid #aaaaaa; background: #ffffff url(im= ages/ui-bg_flat_75_ffffff_40x100.png) 50% 50% repeat-x; color: #222222; } -.ui-widget-content a { color: #222222; } -.ui-widget-header { border: 1px solid #aaaaaa; background: #cccccc url(ima= ges/ui-bg_highlight-soft_75_cccccc_1x100.png) 50% 50% repeat-x; color: #222= 222; font-weight: bold; } -.ui-widget-header a { color: #222222; } - -/* Interaction states -----------------------------------*/ -.ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header= .ui-state-default { border: 1px solid #d3d3d3; background: #e6e6e6 url(ima= ges/ui-bg_glass_75_e6e6e6_1x400.png) 50% 50% repeat-x; font-weight: normal;= color: #555555; } -.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited= { color: #555555; text-decoration: none; } -.ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui= -state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widg= et-header .ui-state-focus { border: 1px solid #999999; background: #dadada = url(images/ui-bg_glass_75_dadada_1x400.png) 50% 50% repeat-x; font-weight: = normal; color: #212121; } -.ui-state-hover a, .ui-state-hover a:hover { color: #212121; text-decorati= on: none; } -.ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .= ui-state-active { border: 1px solid #aaaaaa; background: #ffffff url(images= /ui-bg_glass_65_ffffff_1x400.png) 50% 50% repeat-x; font-weight: normal; co= lor: #212121; } -.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { = color: #212121; text-decoration: none; } -.ui-widget :active { outline: none; } - -/* Interaction Cues -----------------------------------*/ -.ui-state-highlight, .ui-widget-content .ui-state-highlight, .ui-widget-he= ader .ui-state-highlight {border: 1px solid #fcefa1; background: #fbf9ee u= rl(images/ui-bg_glass_55_fbf9ee_1x400.png) 50% 50% repeat-x; color: #363636= ; } -.ui-state-highlight a, .ui-widget-content .ui-state-highlight a,.ui-widget= -header .ui-state-highlight a { color: #363636; } -.ui-state-error, .ui-widget-content .ui-state-error, .ui-widget-header .ui= -state-error {border: 1px solid #cd0a0a; background: #fef1ec url(images/ui-= bg_glass_95_fef1ec_1x400.png) 50% 50% repeat-x; color: #cd0a0a; } -.ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header= .ui-state-error a { color: #cd0a0a; } -.ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-= header .ui-state-error-text { color: #cd0a0a; } -.ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-= header .ui-priority-primary { font-weight: bold; } -.ui-priority-secondary, .ui-widget-content .ui-priority-secondary, .ui-wi= dget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=3D70= ); font-weight: normal; } -.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-head= er .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=3D35); backgroun= d-image: none; } - -/* Icons -----------------------------------*/ - -/* states and images */ -.ui-icon { width: 16px; height: 16px; background-image: url(images/ui-icon= s_222222_256x240.png); } -.ui-widget-content .ui-icon {background-image: url(images/ui-icons_222222_= 256x240.png); } -.ui-widget-header .ui-icon {background-image: url(images/ui-icons_222222_2= 56x240.png); } -.ui-state-default .ui-icon { background-image: url(images/ui-icons_888888_= 256x240.png); } -.ui-state-hover .ui-icon, .ui-state-focus .ui-icon {background-image: url(= images/ui-icons_454545_256x240.png); } -.ui-state-active .ui-icon {background-image: url(images/ui-icons_454545_25= 6x240.png); } -.ui-state-highlight .ui-icon {background-image: url(images/ui-icons_2e83ff= _256x240.png); } -.ui-state-error .ui-icon, .ui-state-error-text .ui-icon {background-image:= url(images/ui-icons_cd0a0a_256x240.png); } - -/* positioning */ -.ui-icon-carat-1-n { background-position: 0 0; } -.ui-icon-carat-1-ne { background-position: -16px 0; } -.ui-icon-carat-1-e { background-position: -32px 0; } -.ui-icon-carat-1-se { background-position: -48px 0; } -.ui-icon-carat-1-s { background-position: -64px 0; } -.ui-icon-carat-1-sw { background-position: -80px 0; } -.ui-icon-carat-1-w { background-position: -96px 0; } -.ui-icon-carat-1-nw { background-position: -112px 0; } -.ui-icon-carat-2-n-s { background-position: -128px 0; } -.ui-icon-carat-2-e-w { background-position: -144px 0; } -.ui-icon-triangle-1-n { background-position: 0 -16px; } -.ui-icon-triangle-1-ne { background-position: -16px -16px; } -.ui-icon-triangle-1-e { background-position: -32px -16px; } -.ui-icon-triangle-1-se { background-position: -48px -16px; } -.ui-icon-triangle-1-s { background-position: -64px -16px; } -.ui-icon-triangle-1-sw { background-position: -80px -16px; } -.ui-icon-triangle-1-w { background-position: -96px -16px; } -.ui-icon-triangle-1-nw { background-position: -112px -16px; } -.ui-icon-triangle-2-n-s { background-position: -128px -16px; } -.ui-icon-triangle-2-e-w { background-position: -144px -16px; } -.ui-icon-arrow-1-n { background-position: 0 -32px; } -.ui-icon-arrow-1-ne { background-position: -16px -32px; } -.ui-icon-arrow-1-e { background-position: -32px -32px; } -.ui-icon-arrow-1-se { background-position: -48px -32px; } -.ui-icon-arrow-1-s { background-position: -64px -32px; } -.ui-icon-arrow-1-sw { background-position: -80px -32px; } -.ui-icon-arrow-1-w { background-position: -96px -32px; } -.ui-icon-arrow-1-nw { background-position: -112px -32px; } -.ui-icon-arrow-2-n-s { background-position: -128px -32px; } -.ui-icon-arrow-2-ne-sw { background-position: -144px -32px; } -.ui-icon-arrow-2-e-w { background-position: -160px -32px; } -.ui-icon-arrow-2-se-nw { background-position: -176px -32px; } -.ui-icon-arrowstop-1-n { background-position: -192px -32px; } -.ui-icon-arrowstop-1-e { background-position: -208px -32px; } -.ui-icon-arrowstop-1-s { background-position: -224px -32px; } -.ui-icon-arrowstop-1-w { background-position: -240px -32px; } -.ui-icon-arrowthick-1-n { background-position: 0 -48px; } -.ui-icon-arrowthick-1-ne { background-position: -16px -48px; } -.ui-icon-arrowthick-1-e { background-position: -32px -48px; } -.ui-icon-arrowthick-1-se { background-position: -48px -48px; } -.ui-icon-arrowthick-1-s { background-position: -64px -48px; } -.ui-icon-arrowthick-1-sw { background-position: -80px -48px; } -.ui-icon-arrowthick-1-w { background-position: -96px -48px; } -.ui-icon-arrowthick-1-nw { background-position: -112px -48px; } -.ui-icon-arrowthick-2-n-s { background-position: -128px -48px; } -.ui-icon-arrowthick-2-ne-sw { background-position: -144px -48px; } -.ui-icon-arrowthick-2-e-w { background-position: -160px -48px; } -.ui-icon-arrowthick-2-se-nw { background-position: -176px -48px; } -.ui-icon-arrowthickstop-1-n { background-position: -192px -48px; } -.ui-icon-arrowthickstop-1-e { background-position: -208px -48px; } -.ui-icon-arrowthickstop-1-s { background-position: -224px -48px; } -.ui-icon-arrowthickstop-1-w { background-position: -240px -48px; } -.ui-icon-arrowreturnthick-1-w { background-position: 0 -64px; } -.ui-icon-arrowreturnthick-1-n { background-position: -16px -64px; } -.ui-icon-arrowreturnthick-1-e { background-position: -32px -64px; } -.ui-icon-arrowreturnthick-1-s { background-position: -48px -64px; } -.ui-icon-arrowreturn-1-w { background-position: -64px -64px; } -.ui-icon-arrowreturn-1-n { background-position: -80px -64px; } -.ui-icon-arrowreturn-1-e { background-position: -96px -64px; } -.ui-icon-arrowreturn-1-s { background-position: -112px -64px; } -.ui-icon-arrowrefresh-1-w { background-position: -128px -64px; } -.ui-icon-arrowrefresh-1-n { background-position: -144px -64px; } -.ui-icon-arrowrefresh-1-e { background-position: -160px -64px; } -.ui-icon-arrowrefresh-1-s { background-position: -176px -64px; } -.ui-icon-arrow-4 { background-position: 0 -80px; } -.ui-icon-arrow-4-diag { background-position: -16px -80px; } -.ui-icon-extlink { background-position: -32px -80px; } -.ui-icon-newwin { background-position: -48px -80px; } -.ui-icon-refresh { background-position: -64px -80px; } -.ui-icon-shuffle { background-position: -80px -80px; } -.ui-icon-transfer-e-w { background-position: -96px -80px; } -.ui-icon-transferthick-e-w { background-position: -112px -80px; } -.ui-icon-folder-collapsed { background-position: 0 -96px; } -.ui-icon-folder-open { background-position: -16px -96px; } -.ui-icon-document { background-position: -32px -96px; } -.ui-icon-document-b { background-position: -48px -96px; } -.ui-icon-note { background-position: -64px -96px; } -.ui-icon-mail-closed { background-position: -80px -96px; } -.ui-icon-mail-open { background-position: -96px -96px; } -.ui-icon-suitcase { background-position: -112px -96px; } -.ui-icon-comment { background-position: -128px -96px; } -.ui-icon-person { background-position: -144px -96px; } -.ui-icon-print { background-position: -160px -96px; } -.ui-icon-trash { background-position: -176px -96px; } -.ui-icon-locked { background-position: -192px -96px; } -.ui-icon-unlocked { background-position: -208px -96px; } -.ui-icon-bookmark { background-position: -224px -96px; } -.ui-icon-tag { background-position: -240px -96px; } -.ui-icon-home { background-position: 0 -112px; } -.ui-icon-flag { background-position: -16px -112px; } -.ui-icon-calendar { background-position: -32px -112px; } -.ui-icon-cart { background-position: -48px -112px; } -.ui-icon-pencil { background-position: -64px -112px; } -.ui-icon-clock { background-position: -80px -112px; } -.ui-icon-disk { background-position: -96px -112px; } -.ui-icon-calculator { background-position: -112px -112px; } -.ui-icon-zoomin { background-position: -128px -112px; } -.ui-icon-zoomout { background-position: -144px -112px; } -.ui-icon-search { background-position: -160px -112px; } -.ui-icon-wrench { background-position: -176px -112px; } -.ui-icon-gear { background-position: -192px -112px; } -.ui-icon-heart { background-position: -208px -112px; } -.ui-icon-star { background-position: -224px -112px; } -.ui-icon-link { background-position: -240px -112px; } -.ui-icon-cancel { background-position: 0 -128px; } -.ui-icon-plus { background-position: -16px -128px; } -.ui-icon-plusthick { background-position: -32px -128px; } -.ui-icon-minus { background-position: -48px -128px; } -.ui-icon-minusthick { background-position: -64px -128px; } -.ui-icon-close { background-position: -80px -128px; } -.ui-icon-closethick { background-position: -96px -128px; } -.ui-icon-key { background-position: -112px -128px; } -.ui-icon-lightbulb { background-position: -128px -128px; } -.ui-icon-scissors { background-position: -144px -128px; } -.ui-icon-clipboard { background-position: -160px -128px; } -.ui-icon-copy { background-position: -176px -128px; } -.ui-icon-contact { background-position: -192px -128px; } -.ui-icon-image { background-position: -208px -128px; } -.ui-icon-video { background-position: -224px -128px; } -.ui-icon-script { background-position: -240px -128px; } -.ui-icon-alert { background-position: 0 -144px; } -.ui-icon-info { background-position: -16px -144px; } -.ui-icon-notice { background-position: -32px -144px; } -.ui-icon-help { background-position: -48px -144px; } -.ui-icon-check { background-position: -64px -144px; } -.ui-icon-bullet { background-position: -80px -144px; } -.ui-icon-radio-off { background-position: -96px -144px; } -.ui-icon-radio-on { background-position: -112px -144px; } -.ui-icon-pin-w { background-position: -128px -144px; } -.ui-icon-pin-s { background-position: -144px -144px; } -.ui-icon-play { background-position: 0 -160px; } -.ui-icon-pause { background-position: -16px -160px; } -.ui-icon-seek-next { background-position: -32px -160px; } -.ui-icon-seek-prev { background-position: -48px -160px; } -.ui-icon-seek-end { background-position: -64px -160px; } -.ui-icon-seek-start { background-position: -80px -160px; } -/* ui-icon-seek-first is deprecated, use ui-icon-seek-start instead */ -.ui-icon-seek-first { background-position: -80px -160px; } -.ui-icon-stop { background-position: -96px -160px; } -.ui-icon-eject { background-position: -112px -160px; } -.ui-icon-volume-off { background-position: -128px -160px; } -.ui-icon-volume-on { background-position: -144px -160px; } -.ui-icon-power { background-position: 0 -176px; } -.ui-icon-signal-diag { background-position: -16px -176px; } -.ui-icon-signal { background-position: -32px -176px; } -.ui-icon-battery-0 { background-position: -48px -176px; } -.ui-icon-battery-1 { background-position: -64px -176px; } -.ui-icon-battery-2 { background-position: -80px -176px; } -.ui-icon-battery-3 { background-position: -96px -176px; } -.ui-icon-circle-plus { background-position: 0 -192px; } -.ui-icon-circle-minus { background-position: -16px -192px; } -.ui-icon-circle-close { background-position: -32px -192px; } -.ui-icon-circle-triangle-e { background-position: -48px -192px; } -.ui-icon-circle-triangle-s { background-position: -64px -192px; } -.ui-icon-circle-triangle-w { background-position: -80px -192px; } -.ui-icon-circle-triangle-n { background-position: -96px -192px; } -.ui-icon-circle-arrow-e { background-position: -112px -192px; } -.ui-icon-circle-arrow-s { background-position: -128px -192px; } -.ui-icon-circle-arrow-w { background-position: -144px -192px; } -.ui-icon-circle-arrow-n { background-position: -160px -192px; } -.ui-icon-circle-zoomin { background-position: -176px -192px; } -.ui-icon-circle-zoomout { background-position: -192px -192px; } -.ui-icon-circle-check { background-position: -208px -192px; } -.ui-icon-circlesmall-plus { background-position: 0 -208px; } -.ui-icon-circlesmall-minus { background-position: -16px -208px; } -.ui-icon-circlesmall-close { background-position: -32px -208px; } -.ui-icon-squaresmall-plus { background-position: -48px -208px; } -.ui-icon-squaresmall-minus { background-position: -64px -208px; } -.ui-icon-squaresmall-close { background-position: -80px -208px; } -.ui-icon-grip-dotted-vertical { background-position: 0 -224px; } -.ui-icon-grip-dotted-horizontal { background-position: -16px -224px; } -.ui-icon-grip-solid-vertical { background-position: -32px -224px; } -.ui-icon-grip-solid-horizontal { background-position: -48px -224px; } -.ui-icon-gripsmall-diagonal-se { background-position: -64px -224px; } -.ui-icon-grip-diagonal-se { background-position: -80px -224px; } - - -/* Misc visuals -----------------------------------*/ - -/* Corner radius */ -.ui-corner-all, .ui-corner-top, .ui-corner-left, .ui-corner-tl { -moz-bord= er-radius-topleft: 4px; -webkit-border-top-left-radius: 4px; -khtml-border-= top-left-radius: 4px; border-top-left-radius: 4px; } -.ui-corner-all, .ui-corner-top, .ui-corner-right, .ui-corner-tr { -moz-bor= der-radius-topright: 4px; -webkit-border-top-right-radius: 4px; -khtml-bord= er-top-right-radius: 4px; border-top-right-radius: 4px; } -.ui-corner-all, .ui-corner-bottom, .ui-corner-left, .ui-corner-bl { -moz-b= order-radius-bottomleft: 4px; -webkit-border-bottom-left-radius: 4px; -khtm= l-border-bottom-left-radius: 4px; border-bottom-left-radius: 4px; } -.ui-corner-all, .ui-corner-bottom, .ui-corner-right, .ui-corner-br { -moz-= border-radius-bottomright: 4px; -webkit-border-bottom-right-radius: 4px; -k= html-border-bottom-right-radius: 4px; border-bottom-right-radius: 4px; } - -/* Overlays */ -.ui-widget-overlay { background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40= x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=3D30); } -.ui-widget-shadow { margin: -8px 0 0 -8px; padding: 8px; background: #aaaa= aa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .3= 0;filter:Alpha(Opacity=3D30); -moz-border-radius: 8px; -khtml-border-radius= : 8px; -webkit-border-radius: 8px; border-radius: 8px; }/*! - * jQuery UI Autocomplete 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Autocomplete#theming - */ -.ui-autocomplete { position: absolute; cursor: default; }=09 - -/* workarounds */ -* html .ui-autocomplete { width:1px; } /* without this, the menu expands t= o 100% in IE6 */ - -/* - * jQuery UI Menu 1.8.23 - * - * Copyright 2010, AUTHORS.txt 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selected.text() : "", + wrapper =3D this.wrapper =3D $( "<span>" ) + .addClass( "ui-combobox" ) + .insertAfter( select ); + + function removeIfInvalid(element) { + var value =3D $( element ).val(), + matcher =3D new RegExp( "^" + $.ui.autocomplete.escape= Regex( value ) + "$", "i" ), + valid =3D false; + select.children( "option" ).each(function() { + if ( $( this ).text().match( matcher ) ) { + this.selected =3D valid =3D true; + return false; + } + }); + if ( !valid ) { + // remove invalid value, as it didn't match anything + $( element ) + .val( "" ) + .attr( "title", value + " didn't match any item" ) + .tooltip( "open" ); + select.val( "" ); + setTimeout(function() { + input.tooltip( "close" ).attr( "title", "" ); + }, 2500 ); + input.data( "autocomplete" ).term =3D ""; + return false; + } + } + + var size =3D ( this.options.size ? this.options.size : 20 ); + input =3D $( "<input>" ) + .appendTo( wrapper ) + .val( value ) + .click( function() { + this.select(); + }) + .attr( "title", "" ) + .attr( "size", size ) + .addClass( "ui-state-default ui-combobox-input" ) + .autocomplete({ + appendTo: this.options.appendTo, + delay: 0, + minLength: 0, + source: function( request, response ) { + var matcher =3D new RegExp( $.ui.autocomplete.esca= peRegex(request.term), "i" ); + response( select.children( "option" ).map(function= () { + var text =3D $( this ).text(); + if ( this.value && ( !request.term || matcher.= test(text) ) ) + return { + label: text.replace( + new RegExp( + "(?![^&;]+;)(?!<[^<>]*)(" + + $.ui.autocomplete.escapeRegex(= request.term) + + ")(?![^<>]*>)(?![^&;]+;)", "gi" + ), "<strong>$1</strong>" ), + value: text, + option: this + }; + }) ); + }, + select: function( event, ui ) { + ui.item.option.selected =3D true; + that._trigger( "selected", event, { + item: ui.item.option + }); + }, + change: function( event, ui ) { + if ( !ui.item ) + return removeIfInvalid( this ); + } + }) + .addClass( "ui-widget ui-widget-content ui-corner-left" ); + + input.data( "autocomplete" )._renderItem =3D function( ul, ite= m ) { + return $( "<li>" ) + .data( "item.autocomplete", item ) + .append( "<a>" + item.label + "</a>" ) + .appendTo( ul ); + }; + + $( "<a>" ) + .attr( "tabIndex", -1 ) + .attr( "title", "Show All Items" ) + .tooltip() + .appendTo( wrapper ) + .button({ + icons: { + primary: "ui-icon-triangle-1-s" + }, + text: false + }) + .removeClass( "ui-corner-all" ) + .addClass( "ui-corner-right ui-combobox-toggle" ) + .click(function() { + // close if already visible + if ( input.autocomplete( "widget" ).is( ":visible" ) )= { + input.autocomplete( "close" ); + removeIfInvalid( input ); + return; + } + + // work around a bug (likely same cause as #5265) + $( this ).blur(); + + // pass empty string as value to search for, displayin= g all results + input.autocomplete( "search", "" ); + input.focus(); + }); + + input + .tooltip({ + position: { + of: this.button + }, + tooltipClass: "ui-state-highlight" + }); + }, + + destroy: function() { + this.wrapper.remove(); + this.element.show(); + $.Widget.prototype.destroy.call( this ); + } + }); +})( jQuery ); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/libs/jquery/jquery-ui.js --- /dev/null +++ b/static/scripts/libs/jquery/jquery-ui.js @@ -0,0 +1,6 @@ +/*! jQuery UI - v1.9.1 - 2012-10-29 +* http://jqueryui.com +* Includes: jquery.ui.core.js, jquery.ui.widget.js, jquery.ui.mouse.js, jq= uery.ui.position.js, jquery.ui.autocomplete.js, jquery.ui.button.js, jquery= .ui.menu.js, jquery.ui.slider.js +* Copyright (c) 2012 jQuery Foundation and other contributors Licensed MIT= */ + +(function(e,t){function i(t,n){var r,i,o,u=3Dt.nodeName.toLowerCase();retu= rn"area"=3D=3D=3Du?(r=3Dt.parentNode,i=3Dr.name,!t.href||!i||r.nodeName.toL= owerCase()!=3D=3D"map"?!1:(o=3De("img[usemap=3D#"+i+"]")[0],!!o&&s(o))):(/i= 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n_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:n= ull,enabled:true,visible:true}});var IconButtonView=3DBackbone.View.extend(= {initialize:function(){this.model.attributes.tooltip_config=3D{placement:"b= ottom"};this.model.bind("change",this.render,this)},render:function(){this.= $el.tooltip("hide");var a=3D$(Handlebars.partials.iconButton(this.model.toJ= SON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a)= ;this.setElement(a);return this},events:{click:"click"},click:function(a){i= f(this.model.attributes.on_click){this.model.attributes.on_click(a);return = false}return true}});IconButtonView.templates=3D{iconButton:Handlebars.part= ials.iconButton};var IconButtonCollection=3DBackbone.Collection.extend({mod= el:IconButton});var IconButtonMenuView=3DBackbone.View.extend({tagName:"div= ",initialize:function(){this.render()},render:function(){var a=3Dthis;this.= collection.each(function(c){var b=3D$("<a/>").attr("href","javascript:void(= 0)").attr("title",c.attributes.title).addClass("icon-button menu-button").a= ddClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_clic= k);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}}= );return this}});var create_icon_buttons_menu=3Dfunction(b,a){if(!a){a=3D{}= }var c=3Dnew IconButtonCollection(_.map(b,function(d){return new IconButton= (_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid= =3DBackbone.Collection.extend({});var GridView=3DBackbone.View.extend({});v= ar GalaxyPaths=3DBackbone.Model.extend({defaults:{root_path:"",image_path:"= "}}); \ No newline at end of file +var IconButton=3DBackbone.Model.extend({defaults:{title:"",icon_class:"",o= n_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,= href:null,target:null,enabled:true,visible:true}});var IconButtonView=3DBac= kbone.View.extend({initialize:function(){this.model.attributes.tooltip_conf= ig=3D{placement:"bottom"};this.model.bind("change",this.render,this)},rende= r:function(){this.$el.tooltip("hide");var a=3D$(Handlebars.partials.iconBut= ton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.= $el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},c= lick:function(a){if(this.model.attributes.on_click){this.model.attributes.o= n_click(a);return false}return true}});IconButtonView.templates=3D{iconButt= on:Handlebars.partials.iconButton};var IconButtonCollection=3DBackbone.Coll= ection.extend({model:IconButton});var IconButtonMenuView=3DBackbone.View.ex= tend({tagName:"div",initialize:function(){this.render()},render:function(){= var a=3Dthis;this.collection.each(function(d){var b=3D$("<a/>").attr("href"= ,"javascript:void(0)").attr("title",d.attributes.title).addClass("icon-butt= on menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.= attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes= .tooltip_config)}var c=3Dd.get("options");if(c){make_popupmenu(b,c)}});retu= rn this}});var create_icon_buttons_menu=3Dfunction(b,a){if(!a){a=3D{}}var c= =3Dnew IconButtonCollection(_.map(b,function(d){return new IconButton(_.ext= end(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=3DBack= bone.Collection.extend({});var GridView=3DBackbone.View.extend({});var Gala= xyPaths=3DBackbone.Model.extend({defaults:{root_path:"",image_path:""}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/visualization"],function(g,j,h){v= ar k=3DBackbone.Model.extend({is_visible:function(o,l){var m=3Do.getBoundin= gClientRect(),n=3D$("svg")[0].getBoundingClientRect();if(m.right<0||m.left>= n.right||m.bottom<0||m.top>n.bottom){return false}return true}});var c=3DBa= ckbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var a=3DBackbone.Vie= w.extend({className:"circster",initialize:function(l){this.total_gap=3Dl.to= tal_gap;this.genome=3Dl.genome;this.dataset_arc_height=3Dl.dataset_arc_heig= ht;this.track_gap=3D5;this.label_arc_height=3D20;this.scale=3D1;this.track_= views=3Dnull;this.model.get("tracks").on("add",this.add_track,this);this.mo= del.get("tracks").on("remove",this.remove_track,this)},get_tracks_bounds:fu= nction(){var n=3Dthis.dataset_arc_height,l=3DMath.min(this.$el.width(),this= .$el.height()),p=3Dl/2-this.model.get("tracks").length*(this.dataset_arc_he= ight+this.track_gap)-(this.label_arc_height+this.track_gap),o=3Dj.range(p,l= /2,this.dataset_arc_height+this.track_gap);var m=3Dthis;return g.map(o,func= tion(q){return[q,q+m.dataset_arc_height]})},render:function(){var o=3Dthis,= q=3Dthis.dataset_arc_height,r=3Do.$el.width(),l=3Do.$el.height(),p=3Dthis.m= odel.get("tracks"),s=3Dthis.get_tracks_bounds(),n=3Dj.select(o.$el[0]).appe= nd("svg").attr("width",r).attr("height",l).attr("pointer-events","all").app= end("svg:g").call(j.behavior.zoom().on("zoom",function(){var t=3Dj.event.sc= ale;n.attr("transform","translate("+j.event.translate+") scale("+t+")");if(= o.scale!=3D=3Dt){if(o.zoom_drag_timeout){clearTimeout(o.zoom_drag_timeout)}= o.zoom_drag_timeout=3DsetTimeout(function(){g.each(o.track_views,function(u= ){u.update_scale(t)})},400)}})).attr("transform","translate("+r/2+","+l/2+"= )").append("svg:g").attr("class","tracks");this.track_views=3Dp.map(functio= n(t,u){track_view_class=3D(t.get("track_type")=3D=3D=3D"LineTrack"?d:e);ret= urn new track_view_class({el:n.append("g")[0],track:t,radius_bounds:s[u],ge= nome:o.genome,total_gap:o.total_gap})});g.each(this.track_views,function(t)= {t.render()});var m=3Ds[p.length];m[1]=3Dm[0];this.label_track_view=3Dnew b= ({el:n.append("g")[0],track:new c(),radius_bounds:m,genome:o.genome,total_g= ap:o.total_gap});this.label_track_view.render()},add_track:function(p){var = o=3Dthis.get_tracks_bounds();g.each(this.track_views,function(r,s){r.update= _radius_bounds(o[s])});var n=3Dthis.track_views.length,q=3D(p.get("track_ty= pe")=3D=3D=3D"LineTrack"?d:e),l=3Dnew q({el:j.select("g.tracks").append("g"= )[0],track:p,radius_bounds:o[n],genome:this.genome,total_gap:this.total_gap= });l.render();this.track_views.push(l);var m=3Do[o.length-1];m[1]=3Dm[0];th= is.label_track_view.update_radius_bounds(m)},remove_track:function(m,o,n){v= ar l=3Dthis.track_views[n.index];this.track_views.splice(n.index,1);l.$el.r= emove();var p=3Dthis.get_tracks_bounds();g.each(this.track_views,function(q= ,r){q.update_radius_bounds(p[r])})}});var i=3DBackbone.View.extend({tagName= :"g",initialize:function(l){this.bg_stroke=3D"ccc";this.loading_bg_fill=3D"= 000";this.bg_fill=3D"ccc";this.total_gap=3Dl.total_gap;this.track=3Dl.track= ;this.radius_bounds=3Dl.radius_bounds;this.genome=3Dl.genome;this.chroms_la= yout=3Dthis._chroms_layout();this.data_bounds=3D[];this.scale=3D1;this.pare= nt_elt=3Dj.select(this.$el[0])},render:function(){var p=3Dthis.parent_elt;i= f(!p){console.log("no parent elt")}var o=3Dthis.chroms_layout,r=3Dj.svg.arc= ().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),l= =3Dp.selectAll("g").data(o).enter().append("svg:g"),n=3Dl.append("path").at= tr("d",r).attr("class","chrom-background").style("stroke",this.bg_stroke).s= tyle("fill",this.loading_bg_fill);n.append("title").text(function(t){return= t.data.chrom});var m=3Dthis,q=3Dm.track.get("data_manager"),s=3D(q?q.data_= is_ready():true);$.when(s).then(function(){$.when(m._render_data(p)).then(f= unction(){n.style("fill",m.bg_fill)})})},update_radius_bounds:function(m){t= his.radius_bounds=3Dm;var l=3Dj.svg.arc().innerRadius(this.radius_bounds[0]= ).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chro= m-background").transition().duration(1000).attr("d",l);this._transition_chr= om_data()},update_scale:function(o){var n=3Dthis.scale;this.scale=3Do;if(o<= =3Dn){return}var m=3Dthis,l=3Dnew k();this.parent_elt.selectAll("path.chrom= -data").filter(function(q,p){return l.is_visible(this)}).each(function(v,r)= {var u=3Dj.select(this),q=3Du.attr("chrom"),t=3Dm.genome.get_chrom_region(q= ),s=3Dm.track.get("data_manager"),p;if(!s.can_get_more_detailed_data(t)){re= turn}p=3Dm.track.get("data_manager").get_more_detailed_data(t,"Coverage",0,= o);$.when(p).then(function(z){u.remove();m._update_data_bounds();var y=3Dg.= find(m.chroms_layout,function(A){return A.data.chrom=3D=3D=3Dq});var w=3Dm.= track.get("prefs"),x=3Dw.block_color;if(!x){x=3Dw.color}m._render_chrom_dat= a(m.parent_elt,y,z).style("stroke",x).style("fill",x)})});return m},_transi= tion_chrom_data:function(){var m=3Dthis.track,o=3Dthis.chroms_layout,l=3Dth= is.parent_elt.selectAll("g>path.chrom-data"),p=3Dl[0].length;if(p>0){var n= =3Dthis;$.when(m.get("data_manager").get_genome_wide_data(this.genome)).the= n(function(r){var q=3Dg.reject(g.map(r,function(s,t){var u=3Dnull,v=3Dn._ge= t_path_function(o[t],s);if(v){u=3Dv(s.data)}return u}),function(s){return s= =3D=3D=3Dnull});l.each(function(t,s){j.select(this).transition().duration(1= 000).attr("d",q[s])})})}},_update_data_bounds:function(){var l=3Dthis.data_= bounds;this.data_bounds=3Dthis.get_data_bounds(this.track.get("data_manager= ").get_genome_wide_data(this.genome));if(this.data_bounds[0]<l[0]||this.dat= a_bounds[1]>l[1]){this._transition_chrom_data()}},_render_data:function(o){= var n=3Dthis,m=3Dthis.chroms_layout,l=3Dthis.track,p=3D$.Deferred();$.when(= l.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){n= .data_bounds=3Dn.get_data_bounds(s);layout_and_data=3Dg.zip(m,s),chroms_dat= a_layout=3Dg.map(layout_and_data,function(t){var u=3Dt[0],v=3Dt[1];return n= ._render_chrom_data(o,u,v)});var q=3Dl.get("config"),r=3Dq.get_value("block= _color");if(!r){r=3Dq.get_value("color")}n.parent_elt.selectAll("path.chrom= -data").style("stroke",r).style("fill",r);p.resolve(o)});return p},_render_= chrom_data:function(l,m,n){},_get_path_function:function(m,l){},_chroms_lay= out:function(){var m=3Dthis.genome.get_chroms_info(),o=3Dj.layout.pie().val= ue(function(q){return q.len}).sort(null),p=3Do(m),l=3Dthis.total_gap/m.leng= th,n=3Dg.map(p,function(s,r){var q=3Ds.endAngle-l;s.endAngle=3D(q>s.startAn= gle?q:s.startAngle);return s});return n}});var b=3Di.extend({initialize:fun= ction(l){i.prototype.initialize.call(this,l);this.bg_stroke=3D"fff";this.bg= _fill=3D"fff"},_render_data:function(m){var l=3Dm.selectAll("g");l.selectAl= l("path").attr("id",function(n){return"label-"+n.data.chrom});l.append("svg= :text").filter(function(n){return n.endAngle-n.startAngle>0.08}).attr("text= -anchor","middle").append("svg:textPath").attr("xlink:href",function(n){ret= urn"#label-"+n.data.chrom}).attr("startOffset","25%").text(function(n){retu= rn n.data.chrom})}});var f=3Di.extend({_render_chrom_data:function(l,o,m){v= ar p=3Dthis._get_path_function(o,m);if(!p){return null}var n=3Dl.datum(m.da= ta),q=3Dn.append("path").attr("class","chrom-data").attr("chrom",o.data.chr= om).attr("d",p);return q},_get_path_function:function(o,n){if(typeof n=3D= =3D=3D"string"||!n.data||n.data.length=3D=3D=3D0){return null}var l=3Dj.sca= le.linear().domain(this.data_bounds).range(this.radius_bounds);var p=3Dj.sc= ale.linear().domain([0,n.data.length]).range([o.startAngle,o.endAngle]);var= m=3Dj.svg.line.radial().interpolate("linear").radius(function(q){return l(= q[1])}).angle(function(r,q){return p(q)});return j.svg.area.radial().interp= olate(m.interpolate()).innerRadius(l(0)).outerRadius(m.radius()).angle(m.an= gle())},get_data_bounds:function(l){}});var e=3Df.extend({get_data_bounds:f= unction(m){var l=3Dg.map(m,function(n){if(typeof n=3D=3D=3D"string"||!n.max= ){return 0}return n.max});return[0,(l&&typeof l!=3D=3D"string"?g.max(l):0)]= }});var d=3Df.extend({get_data_bounds:function(m){var l=3Dg.flatten(g.map(m= ,function(n){if(n){return g.map(n.data,function(o){return o[1]})}else{retur= n 0}}));return[g.min(l),g.max(l)]}});return{CircsterView:a}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,k,h){v= ar l=3DBackbone.Model.extend({is_visible:function(p,m){var n=3Dp.getBoundin= gClientRect(),o=3D$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>= o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var c=3DBa= ckbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var a=3DBackbone.Vie= w.extend({className:"circster",initialize:function(m){this.total_gap=3Dm.to= tal_gap;this.genome=3Dm.genome;this.dataset_arc_height=3Dm.dataset_arc_heig= ht;this.track_gap=3D5;this.label_arc_height=3D20;this.scale=3D1;this.circul= ar_views=3Dnull;this.chords_views=3Dnull;this.model.get("tracks").on("add",= this.add_track,this);this.model.get("tracks").on("remove",this.remove_track= ,this);this.get_circular_tracks()},get_circular_tracks:function(){return th= is.model.get("tracks").filter(function(m){return m.get("track_type")!=3D=3D= "DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get= ("tracks").filter(function(m){return m.get("track_type")=3D=3D=3D"DiagonalH= eatmapTrack"})},get_tracks_bounds:function(){var n=3Dthis.get_circular_trac= ks();dataset_arc_height=3Dthis.dataset_arc_height,min_dimension=3DMath.min(= this.$el.width(),this.$el.height()),radius_start=3Dmin_dimension/2-n.length= *(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track= _gap),tracks_start_radii=3Dk.range(radius_start,min_dimension/2,this.datase= t_arc_height+this.track_gap);var m=3Dthis;return g.map(tracks_start_radii,f= unction(o){return[o,o+m.dataset_arc_height]})},render:function(){var u=3Dth= is,p=3Dthis.dataset_arc_height,m=3Du.$el.width(),t=3Du.$el.height(),r=3Dthi= s.get_circular_tracks(),o=3Dthis.get_chord_tracks(),q=3Dthis.get_tracks_bou= nds(),n=3Dk.select(u.$el[0]).append("svg").attr("width",m).attr("height",t)= .attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zo= om",function(){var v=3Dk.event.scale;n.attr("transform","translate("+k.even= t.translate+") scale("+v+")");if(u.scale!=3D=3Dv){if(u.zoom_drag_timeout){c= learTimeout(u.zoom_drag_timeout)}u.zoom_drag_timeout=3DsetTimeout(function(= ){g.each(u.circular_views,function(w){w.update_scale(v)})},400)}})).attr("t= ransform","translate("+m/2+","+t/2+")").append("svg:g").attr("class","track= s");this.circular_views=3Dr.map(function(w,x){var y=3D(w.get("track_type")= =3D=3D=3D"LineTrack"?d:e),v=3Dnew y({el:n.append("g")[0],track:w,radius_bou= nds:q[x],genome:u.genome,total_gap:u.total_gap});v.render();return v});this= .chords_views=3Do.map(function(w){var v=3Dnew i({el:n.append("g")[0],track:= w,radius_bounds:q[0],genome:u.genome,total_gap:u.total_gap});v.render();ret= urn v});var s=3Dq[r.length];s[1]=3Ds[0];this.label_track_view=3Dnew b({el:n= .append("g")[0],track:new c(),radius_bounds:s,genome:u.genome,total_gap:u.t= otal_gap});this.label_track_view.render()},add_track:function(s){if(s.get("= track_type")=3D=3D=3D"DiagonalHeatmapTrack"){var o=3Dthis.circular_views[0]= .radius_bounds,r=3Dnew i({el:k.select("g.tracks").append("g")[0],track:s,ra= dius_bounds:o,genome:this.genome,total_gap:this.total_gap});r.render();this= .chords_views.push(r)}else{var q=3Dthis.get_tracks_bounds();g.each(this.cir= cular_views,function(u,v){u.update_radius_bounds(q[v])});g.each(this.chords= _views,function(u){u.update_radius_bounds(q[0])});var p=3Dthis.circular_vie= ws.length,t=3D(s.get("track_type")=3D=3D=3D"LineTrack"?d:e),m=3Dnew t({el:k= .select("g.tracks").append("g")[0],track:s,radius_bounds:q[p],genome:this.g= enome,total_gap:this.total_gap});m.render();this.circular_views.push(m);var= n=3Dq[q.length-1];n[1]=3Dn[0];this.label_track_view.update_radius_bounds(n= )}},remove_track:function(n,p,o){var m=3Dthis.circular_views[o.index];this.= circular_views.splice(o.index,1);m.$el.remove();var q=3Dthis.get_tracks_bou= nds();g.each(this.circular_views,function(r,s){r.update_radius_bounds(q[s])= })}});var j=3DBackbone.View.extend({tagName:"g",initialize:function(m){this= .bg_stroke=3D"ccc";this.loading_bg_fill=3D"000";this.bg_fill=3D"ccc";this.t= otal_gap=3Dm.total_gap;this.track=3Dm.track;this.radius_bounds=3Dm.radius_b= ounds;this.genome=3Dm.genome;this.chroms_layout=3Dthis._chroms_layout();thi= s.data_bounds=3D[];this.scale=3D1;this.parent_elt=3Dk.select(this.$el[0])},= get_fill_color:function(){var m=3Dthis.track.get("config").get_value("block= _color");if(!m){m=3Dthis.track.get("config").get_value("color")}return m},r= ender:function(){var q=3Dthis.parent_elt;if(!q){console.log("no parent elt"= )}var p=3Dthis.chroms_layout,s=3Dk.svg.arc().innerRadius(this.radius_bounds= [0]).outerRadius(this.radius_bounds[1]),m=3Dq.selectAll("g").data(p).enter(= ).append("svg:g"),o=3Dm.append("path").attr("d",s).attr("class","chrom-back= ground").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);= o.append("title").text(function(u){return u.data.chrom});var n=3Dthis,r=3Dn= .track.get("data_manager"),t=3D(r?r.data_is_ready():true);$.when(t).then(fu= nction(){$.when(n._render_data(q)).then(function(){o.style("fill",n.bg_fill= )})})},update_radius_bounds:function(n){this.radius_bounds=3Dn;var m=3Dk.sv= g.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1= ]);this.parent_elt.selectAll("g>path.chrom-background").transition().durati= on(1000).attr("d",m);this._transition_chrom_data()},update_scale:function(p= ){var o=3Dthis.scale;this.scale=3Dp;if(p<=3Do){return}var n=3Dthis,m=3Dnew = l();this.parent_elt.selectAll("path.chrom-data").filter(function(r,q){retur= n m.is_visible(this)}).each(function(w,s){var v=3Dk.select(this),r=3Dv.attr= ("chrom"),u=3Dn.genome.get_chrom_region(r),t=3Dn.track.get("data_manager"),= q;if(!t.can_get_more_detailed_data(u)){return}q=3Dn.track.get("data_manager= ").get_more_detailed_data(u,"Coverage",0,p);$.when(q).then(function(z){v.re= move();n._update_data_bounds();var y=3Dg.find(n.chroms_layout,function(A){r= eturn A.data.chrom=3D=3D=3Dr});var x=3Dn.get_fill_color();n._render_chrom_d= ata(n.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_tran= sition_chrom_data:function(){var n=3Dthis.track,p=3Dthis.chroms_layout,m=3D= this.parent_elt.selectAll("g>path.chrom-data"),q=3Dm[0].length;if(q>0){var = o=3Dthis;$.when(n.get("data_manager").get_genome_wide_data(this.genome)).th= en(function(s){var r=3Dg.reject(g.map(s,function(t,u){var v=3Dnull,w=3Do._g= et_path_function(p[u],t);if(w){v=3Dw(t.data)}return v}),function(t){return = t=3D=3D=3Dnull});m.each(function(u,t){k.select(this).transition().duration(= 1000).attr("d",r[t])})})}},_update_data_bounds:function(){var m=3Dthis.data= _bounds;this.data_bounds=3Dthis.get_data_bounds(this.track.get("data_manage= r").get_genome_wide_data(this.genome));if(this.data_bounds[0]<m[0]||this.da= ta_bounds[1]>m[1]){this._transition_chrom_data()}},_render_data:function(p)= {var o=3Dthis,n=3Dthis.chroms_layout,m=3Dthis.track,q=3D$.Deferred();$.when= (m.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){= o.data_bounds=3Do.get_data_bounds(s);layout_and_data=3Dg.zip(n,s),chroms_da= ta_layout=3Dg.map(layout_and_data,function(t){var u=3Dt[0],v=3Dt[1];return = o._render_chrom_data(p,u,v)});var r=3Do.get_fill_color();o.parent_elt.selec= tAll("path.chrom-data").style("stroke",r).style("fill",r);q.resolve(p)});re= turn q},_render_chrom_data:function(m,n,o){},_get_path_function:function(n,= m){},_chroms_layout:function(){var n=3Dthis.genome.get_chroms_info(),p=3Dk.= layout.pie().value(function(r){return r.len}).sort(null),q=3Dp(n),m=3Dthis.= total_gap/n.length,o=3Dg.map(q,function(t,s){var r=3Dt.endAngle-m;t.endAngl= e=3D(r>t.startAngle?r:t.startAngle);return t});return o}});var b=3Dj.extend= ({initialize:function(m){j.prototype.initialize.call(this,m);this.bg_stroke= =3D"fff";this.bg_fill=3D"fff"},_render_data:function(n){var m=3Dn.selectAll= ("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom= });m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0= .08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href"= ,function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(= function(o){return o.data.chrom})}});var f=3Dj.extend({_render_chrom_data:f= unction(m,p,n){var q=3Dthis._get_path_function(p,n);if(!q){return null}var = o=3Dm.datum(n.data),r=3Do.append("path").attr("class","chrom-data").attr("c= hrom",p.data.chrom).attr("d",q);return r},_get_path_function:function(p,o){= if(typeof o=3D=3D=3D"string"||!o.data||o.data.length=3D=3D=3D0){return null= }var m=3Dk.scale.linear().domain(this.data_bounds).range(this.radius_bounds= );var q=3Dk.scale.linear().domain([0,o.data.length]).range([p.startAngle,p.= endAngle]);var n=3Dk.svg.line.radial().interpolate("linear").radius(functio= n(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.r= adial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius= ()).angle(n.angle())},get_data_bounds:function(m){}});var e=3Df.extend({get= _data_bounds:function(n){var m=3Dg.map(n,function(o){if(typeof o=3D=3D=3D"s= tring"||!o.max){return 0}return o.max});return[0,(m&&typeof m!=3D=3D"string= "?g.max(m):0)]}});var d=3Df.extend({get_data_bounds:function(n){var m=3Dg.f= latten(g.map(n,function(o){if(o){return g.map(o.data,function(q){return q[1= ]})}else{return 0}}));return[g.min(m),g.max(m)]}});var i=3Dj.extend({render= :function(){var m=3Dthis;$.when(m.track.get("data_manager").data_is_ready()= ).then(function(){$.when(m.track.get("data_manager").get_genome_wide_data(m= .genome)).then(function(p){var o=3D[],n=3Dm.genome.get_chroms_info();g.each= (p,function(t,s){var q=3Dn[s].chrom;var r=3Dg.map(t.data,function(v){var u= =3Dm._get_region_angle(q,v[1]),w=3Dm._get_region_angle(v[3],v[4]);return{so= 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-define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","= ../templates/compiled/template-visualization-scatterplotControlForm","../te= mplates/compiled/template-visualization-statsTable","../templates/compiled/= template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../= libs/jquery/jquery-ui-1.8.23.custom.min"],function(){function a(f){var d=3D= 10,h=3D7,g=3D10,e=3D8,c=3D5;this.log=3Dfunction(){if(this.debugging&&consol= e&&console.debug){var i=3DArray.prototype.slice.call(arguments);i.unshift(t= his.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatte= rplot:",f);this.defaults=3D{id:"TwoVarScatterplot",containerSelector:"body"= ,maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTick= s:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:= 50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:nu= ll,yMax:null,xLabel:"X",yLabel:"Y"};this.config=3D_.extend({},this.defaults= 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X).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transf= orm",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).= text(this.config.yLabel)};this.renderGrid=3Dfunction(){this.vGridLines=3Dth= is.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisF= n.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-lin= e v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).at= tr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().r= emove();this.hGridLines=3Dthis.content.selectAll("line.h-grid-line").data(t= his.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("= svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",= 0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScal= e);this.hGridLines.exit().remove()};this.glyphEnterState=3Dfunction(i){};th= is.glyphFinalState=3Dfunction(i){};this.glyphExitState=3Dfunction(i){};this= 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apiDatasetsURL")}else{this.dataURL=3Dc.apiDatasetsURL+"/"+this.dataset.id+"= ?"}this.log("this.dataURL:",this.dataURL)},initializeChart:function(c){this= .chartConfig=3Dc.chartConfig||{};if(this.logger){this.chartConfig.debugging= =3Dtrue}this.log("initial chartConfig:",this.chartConfig);this.plot=3Dnew a= (this.chartConfig);this.chartConfig=3Dthis.plot.config},initializeDataLoade= r:function(d){var c=3Dthis;this.loader=3Dnew LazyDataLoader({logger:(this.l= ogger)?(this.logger):(null),url:null,start:d.start||0,total:d.total||this.d= ataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,= buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_va= ls:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);a= lert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:= function(){var c=3Dthis,d=3D{config:this.chartConfig,allColumns:[],numericC= olumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this= .loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(= g,f){var e=3D"column "+(f+1);if(c.dataset.metadata_column_names){e=3Dc.data= set.metadata_column_names[f]}if(g=3D=3D=3D"int"||g=3D=3D=3D"float"){d.numer= icColumns.push({index:f,name:e})}d.allColumns.push({index:f,name:e})});this= .$el.append(b.templates.form(d));this.$dataSettingsPanel=3Dthis.$el.find(".= tab-pane#data-settings");this.$chartSettingsPanel=3Dthis._render_chartSetti= ngs();this.$statsPanel=3Dthis.$el.find(".tab-pane#chart-stats");return this= },_render_chartSettings:function(){var c=3Dthis,d=3Dthis.$el.find(".tab-pan= e#chart-settings"),e=3D{datapointSize:{min:2,max:10,step:1},width:{min:200,= max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.cha= rtSettings(this.chartConfig));d.find(".numeric-slider-input").each(function= (){var h=3D$(this),g=3Dh.find(".slider-output"),i=3Dh.find(".slider"),j=3Dh= .attr("id");function f(){var l=3D$(this),k=3Dl.slider("value");g.text(k)}i.= slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d= },events:{"click #include-id-checkbox":"toggleThirdColumnSelector","click #= data-settings #render-button":"renderPlot","click #chart-settings #render-b= utton":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el= .find('select[name=3D"ID"]').parent().toggle()},showLoadingIndicator:functi= on(d,e){d=3Dd||"";var c=3Dthis.$el.find("div#loading-indicator");messageBox= =3Dc.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut= ("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e(= )}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:= function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},rende= rPlot:function(){var c=3Dthis;c.data=3Dnull;c.meta=3Dnull;_.extend(this.cha= rtConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartCo= nfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=3Dthis= .dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, ur= l:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded= .new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse= (d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicat= or("Rendering...",function(){c.$el.find("ul.nav").find('a[href=3D"#chart-st= ats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.met= a);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e= ){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetchi= ng data...",function(){c.loader.load()})},renderStats:function(){this.$stat= sPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].= count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.= meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name= :"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.= meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].media= n,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=3Dthi= s;newGraphSettings=3Dthis.getGraphSettings();this.log("newGraphSettings:",n= ewGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this= .chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,fa= lse);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.= plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot(= )}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);t= his.postProcessMeta(c.meta)},postProcessData:function(d){var c=3Dthis;if(c.= data){_.each(d,function(f,e){c.data[e]=3Dc.data[e].concat(f)})}else{c.data= =3Dd}},postProcessMeta:function(e){var c=3Dthis,d=3Dthis.dataset.metadata_c= olumn_types;if(c.meta){_.each(e,function(g,f){var k=3Dc.meta[f],i=3Dd[f];c.= log(f+" postprocessing meta:",g);k.count+=3D(g.count)?(g.count):(0);c.log(f= ,"count:",k.count);if((i=3D=3D=3D"int")||(i=3D=3D=3D"float")){k.min=3DMath.= min(g.min,k.min);k.max=3DMath.max(g.max,k.max);k.sum=3Dg.sum+k.sum;k.mean= =3D(k.count)?(k.sum/k.count):(null);var h=3Dc.data[f].slice().sort(),j=3DMa= th.floor(h.length/2);if(h.length%2=3D=3D=3D0){k.median=3D((h[j]+h[(j+1)])/2= )}else{k.median=3Dh[j]}}})}else{c.meta=3De;c.log("initial meta:",c.meta)}},= getDataSettings:function(){var d=3Dthis.getColumnSelections(),c=3D[];this.l= og("columnSelections:",d);c=3D[d.X.colIndex,d.Y.colIndex];if(this.$dataSett= ingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colInde= x)}var e=3D{data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);r= eturn e},getColumnSelections:function(){var c=3D{};this.$dataSettingsPanel.= find("div.column-select select").each(function(){var d=3D$(this),e=3Dd.val(= );c[d.attr("name")]=3D{colIndex:e,colName:d.children('[value=3D"'+e+'"]').t= ext()}});return c},getGraphSettings:function(){var e=3D{},f=3Dthis.getColum= nSelections();e.datapointSize=3Dthis.$chartSettingsPanel.find("#datapointSi= ze.numeric-slider-input").find(".slider").slider("value");e.width=3Dthis.$c= hartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slide= r("value");e.height=3Dthis.$chartSettingsPanel.find("#height.numeric-slider= -input").find(".slider").slider("value");var d=3Dthis.$chartSettingsPanel.f= ind("input#X-axis-label").val(),c=3Dthis.$chartSettingsPanel.find("input#Y-= axis-label").val();e.xLabel=3D(d=3D=3D=3D"X")?(f.X.colName):(d);e.yLabel=3D= (c=3D=3D=3D"Y")?(f.Y.colName):(c);e.animDuration=3D10;if(this.$chartSetting= sPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration= =3D500}this.log("graphSettings:",e);return e},toString:function(){return"Sc= atterplotControlForm("+this.dataset.id+")"}});b.templates=3D{form:Handlebar= s.templates["template-visualization-scatterplotControlForm"],statsTable:Han= dlebars.templates["template-visualization-statsTable"],chartSettings:Handle= bars.templates["template-visualization-chartSettings"]};return{LazyDataLoad= er:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file +define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","= ../templates/compiled/template-visualization-scatterplotControlForm","../te= mplates/compiled/template-visualization-statsTable","../templates/compiled/= template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../= libs/jquery/jquery-ui"],function(){function a(f){var d=3D10,h=3D7,g=3D10,e= =3D8,c=3D5;this.log=3Dfunction(){if(this.debugging&&console&&console.debug)= {var i=3DArray.prototype.slice.call(arguments);i.unshift(this.toString());c= onsole.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.d= efaults=3D{id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30= 000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBu= mpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50= ,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLab= el:"X",yLabel:"Y"};this.config=3D_.extend({},this.defaults,f);this.updateCo= nfig=3Dfunction(i,j){_.extend(this.config,i)};this.toString=3Dfunction(){re= turn this.config.id};this.translateStr=3Dfunction(i,j){return"translate("+i= +","+j+")"};this.rotateStr=3Dfunction(j,i,k){return"rotate("+j+","+i+","+k+= ")"};this.svg=3Dd3.select(this.config.containerSelector).append("svg:svg").= attr("class","chart");this.content=3Dthis.svg.append("svg:g").attr("class",= "content").attr("id",this.config.id);this.xAxis=3Dthis.content.append("g").= attr("class","axis").attr("id","x-axis");this.xAxisLabel=3Dthis.xAxis.appen= d("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis= =3Dthis.content.append("g").attr("class","axis").attr("id","y-axis");this.y= AxisLabel=3Dthis.yAxis.append("text").attr("class","axis-label").attr("id",= "y-axis-label");this.adjustChartDimensions=3Dfunction(l,j,i,k){l=3Dl||0;j= =3Dj||0;i=3Di||0;k=3Dk||0;this.svg.attr("width",this.config.width+(this.con= fig.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.he= ight+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display= ","block");this.content=3Dthis.svg.select("g.content").attr("transform",thi= s.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.pre= processData=3Dfunction(k,j,i){return(k.length>this.config.maxDataPoints)?(k= .slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=3Dfunction(i,k,= j){this.xMin=3Dthis.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=3Dthi= s.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=3Dthis.config.yMin||(j)= ?(j[1].min):(d3.min(k));this.yMax=3Dthis.config.yMax||(j)?(j[1].max):(d3.ma= x(k))};this.setUpScales=3Dfunction(){this.xScale=3Dd3.scale.linear().domain= ([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=3Dd3.scale= .linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this= .setUpXAxis=3Dfunction(){this.xAxisFn=3Dd3.svg.axis().scale(this.xScale).ti= cks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",thi= s.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel= =3Dd3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}= ));if(this.xLongestLabel>=3Dc){this.xAxis.selectAll("g").filter(":nth-child= (odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/= 2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(= this.config.xLabel)};this.setUpYAxis=3Dfunction(){this.yAxisFn=3Dd3.svg.axi= s().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAx= is.call(this.yAxisFn);var i=3Dthis.yAxis.selectAll("text").filter(function(= m,l){return l!=3D=3D0});this.yLongestLabel=3Dd3.max(i[0].map(function(m,l){= return(d3.select(m).text()).length}))||0;var j=3Dd+(this.yLongestLabel*h)+e= +g;this.config.yAxisLabelBumpX=3D-(j-g);if(this.config.marginLeft<j){var k= =3D(j)-this.config.marginLeft;k=3D(k<0)?(0):(k);this.adjustChartDimensions(= 0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",thi= s.config.height/2).attr("text-anchor","middle").attr("transform",this.rotat= eStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.confi= g.yLabel)};this.renderGrid=3Dfunction(){this.vGridLines=3Dthis.content.sele= ctAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));= this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",= true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xS= cale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hG= ridLines=3Dthis.content.selectAll("line.h-grid-line").data(this.yScale.tick= s(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").clas= sed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",th= is.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLi= nes.exit().remove()};this.glyphEnterState=3Dfunction(i){};this.glyphFinalSt= ate=3Dfunction(i){};this.glyphExitState=3Dfunction(i){};this.renderDatapoin= ts=3Dfunction(i,l,j){this.log(this+".renderDatapoints",arguments);var k=3D0= ;this.datapoints=3Dthis.addDatapoints(i,l,j,".glyph");this.datapoints.exit(= ).each(function(){k+=3D1}).transition().duration(this.config.animDuration).= attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs remo= ved")};this.addDatapoints=3Dfunction(m,k,i,l){this.log(this+".addDatapoints= ",arguments);var p=3Dthis,o=3D0,q=3Dfunction(s,r){return p.xScale(m[r])},j= =3Dfunction(s,r){return p.yScale(k[r])};var n=3Dthis.content.selectAll(l);t= his.log("existing datapoints:",n);n=3Dn.data(m);o=3D0;n.enter().append("svg= :circle").each(function(){o+=3D1}).classed("glyph",true).attr("cx",q).attr(= "cy",j).attr("r",0);this.log(o," new glyphs created");o=3D0;n.transition().= duration(this.config.animDuration).each(function(){o+=3D1}).attr("cx",q).at= tr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs tr= ansitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title= ",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseov= er",function(){var r=3Dd3.select(this);r.style("fill","red").style("fill-op= acity",1);p.content.append("line").attr("stroke","red").attr("stroke-width"= ,1).attr("x1",r.attr("cx")).attr("y1",r.attr("cy")).attr("x2",0).attr("y2",= r.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stro= ke","red").attr("stroke-width",1).attr("x1",r.attr("cx")).attr("y1",r.attr(= "cy")).attr("x2",r.attr("cx")).attr("y2",p.config.height).classed("hoverlin= e",true)}).on("mouseout",function(){d3.select(this).style("fill","black").s= tyle("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};th= is.render=3Dfunction(k,l){this.log(this+".render",arguments);var i=3Dk[0],m= =3Dk[1],j=3D(k.length>2)?(k[2]):(undefined);i=3Dthis.preprocessData(i);m=3D= this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);th= is.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this= .setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m= ,j)}}var b=3DBaseView.extend(LoggableMixin).extend({className:"scatterplot-= settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"l= oading_large_white_bg.gif",initialize:function(c){if(this.logger){window.fo= rm=3Dthis}this.dataset=3Dnull;this.chartConfig=3Dnull;this.plot=3Dnull;this= .loader=3Dnull;this.$statsPanel=3Dnull;this.$chartSettingsPanel=3Dnull;this= .$dataSettingsPanel=3Dnull;this.dataFetch=3Dnull;this.initializeFromAttribu= tes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFrom= Attributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires = a dataset")}else{this.dataset=3Dc.dataset}if(jQuery.type(this.dataset.metad= ata_column_types)=3D=3D=3D"string"){this.dataset.metadata_column_types=3Dth= is.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.datas= et);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL= ")}else{this.dataURL=3Dc.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("t= his.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig= =3Dc.chartConfig||{};if(this.logger){this.chartConfig.debugging=3Dtrue}this= .log("initial chartConfig:",this.chartConfig);this.plot=3Dnew a(this.chartC= onfig);this.chartConfig=3Dthis.plot.config},initializeDataLoader:function(d= ){var c=3Dthis;this.loader=3Dnew LazyDataLoader({logger:(this.logger)?(this= .logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metad= ata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:fun= ction(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(= this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR = fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){v= ar c=3Dthis,d=3D{config:this.chartConfig,allColumns:[],numericColumns:[],lo= adingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndi= catorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e= =3D"column "+(f+1);if(c.dataset.metadata_column_names){e=3Dc.dataset.metada= ta_column_names[f]}if(g=3D=3D=3D"int"||g=3D=3D=3D"float"){d.numericColumns.= push({index:f,name:e})}d.allColumns.push({index:f,name:e})});this.$el.appen= d(b.templates.form(d));this.$dataSettingsPanel=3Dthis.$el.find(".tab-pane#d= ata-settings");this.$chartSettingsPanel=3Dthis._render_chartSettings();this= .$statsPanel=3Dthis.$el.find(".tab-pane#chart-stats");return this},_render_= chartSettings:function(){var c=3Dthis,d=3Dthis.$el.find(".tab-pane#chart-se= ttings"),e=3D{datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,st= ep:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings= (this.chartConfig));d.find(".numeric-slider-input").each(function(){var h= =3D$(this),g=3Dh.find(".slider-output"),i=3Dh.find(".slider"),j=3Dh.attr("i= d");function f(){var l=3D$(this),k=3Dl.slider("value");g.text(k)}i.slider(_= .extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events= :{"click #include-id-checkbox":"toggleThirdColumnSelector","click #data-set= tings #render-button":"renderPlot","click #chart-settings #render-button":"= changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('s= elect[name=3D"ID"]').parent().toggle()},showLoadingIndicator:function(d,e){= d=3Dd||"";var c=3Dthis.$el.find("div#loading-indicator");messageBox=3Dc.fin= d(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",= function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{= if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function= (c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:fu= nction(){var c=3Dthis;c.data=3Dnull;c.meta=3Dnull;_.extend(this.chartConfig= ,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);th= is.plot.updateConfig(this.chartConfig,false);this.loader.url=3Dthis.dataURL= +"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this= .loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",fu= nction(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.lo= g("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rend= ering...",function(){c.$el.find("ul.nav").find('a[href=3D"#chart-stats"]').= tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hid= eLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log(= "complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data.= ..",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.h= tml(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yv= al:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].= min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",x= val:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].= mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:t= his.meta[1].median}]}))},changeChartSettings:function(){var c=3Dthis;newGra= phSettings=3Dthis.getGraphSettings();this.log("newGraphSettings:",newGraphS= ettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartCo= nfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(= c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.ren= der(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},post= ProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.post= ProcessMeta(c.meta)},postProcessData:function(d){var c=3Dthis;if(c.data){_.= each(d,function(f,e){c.data[e]=3Dc.data[e].concat(f)})}else{c.data=3Dd}},po= stProcessMeta:function(e){var c=3Dthis,d=3Dthis.dataset.metadata_column_typ= es;if(c.meta){_.each(e,function(g,f){var k=3Dc.meta[f],i=3Dd[f];c.log(f+" p= ostprocessing meta:",g);k.count+=3D(g.count)?(g.count):(0);c.log(f,"count:"= ,k.count);if((i=3D=3D=3D"int")||(i=3D=3D=3D"float")){k.min=3DMath.min(g.min= ,k.min);k.max=3DMath.max(g.max,k.max);k.sum=3Dg.sum+k.sum;k.mean=3D(k.count= )?(k.sum/k.count):(null);var h=3Dc.data[f].slice().sort(),j=3DMath.floor(h.= length/2);if(h.length%2=3D=3D=3D0){k.median=3D((h[j]+h[(j+1)])/2)}else{k.me= dian=3Dh[j]}}})}else{c.meta=3De;c.log("initial meta:",c.meta)}},getDataSett= ings:function(){var d=3Dthis.getColumnSelections(),c=3D[];this.log("columnS= elections:",d);c=3D[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.f= ind("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e=3D= {data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},ge= tColumnSelections:function(){var c=3D{};this.$dataSettingsPanel.find("div.c= olumn-select select").each(function(){var d=3D$(this),e=3Dd.val();c[d.attr(= "name")]=3D{colIndex:e,colName:d.children('[value=3D"'+e+'"]').text()}});re= turn c},getGraphSettings:function(){var e=3D{},f=3Dthis.getColumnSelections= ();e.datapointSize=3Dthis.$chartSettingsPanel.find("#datapointSize.numeric-= slider-input").find(".slider").slider("value");e.width=3Dthis.$chartSetting= sPanel.find("#width.numeric-slider-input").find(".slider").slider("value");= e.height=3Dthis.$chartSettingsPanel.find("#height.numeric-slider-input").fi= nd(".slider").slider("value");var d=3Dthis.$chartSettingsPanel.find("input#= X-axis-label").val(),c=3Dthis.$chartSettingsPanel.find("input#Y-axis-label"= ).val();e.xLabel=3D(d=3D=3D=3D"X")?(f.X.colName):(d);e.yLabel=3D(c=3D=3D=3D= "Y")?(f.Y.colName):(c);e.animDuration=3D10;if(this.$chartSettingsPanel.find= ("#animDuration.checkbox-input").is(":checked")){e.animDuration=3D500}this.= log("graphSettings:",e);return e},toString:function(){return"ScatterplotCon= trolForm("+this.dataset.id+")"}});b.templates=3D{form:Handlebars.templates[= "template-visualization-scatterplotControlForm"],statsTable:Handlebars.temp= lates["template-visualization-statsTable"],chartSettings:Handlebars.templat= es["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataL= oader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=3D_.extend;var BEFORE=3D= 1001,CONTAINS=3D1002,OVERLAP_START=3D1003,OVERLAP_END=3D1004,CONTAINED_BY= =3D1005,AFTER=3D1006;var compute_overlap=3Dfunction(first_region,second_reg= ion){var first_start=3Dfirst_region[0],first_end=3Dfirst_region[1],second_s= tart=3Dsecond_region[0],second_end=3Dsecond_region[1],overlap;if(first_star= t<second_start){if(first_end<second_start){overlap=3DBEFORE}else{if(first_e= nd<=3Dsecond_end){overlap=3DOVERLAP_START}else{overlap=3DCONTAINS}}}else{if= (first_start>second_end){overlap=3DAFTER}else{if(first_end<=3Dsecond_end){o= verlap=3DCONTAINED_BY}else{overlap=3DOVERLAP_END}}}return overlap};var is_o= verlap=3Dfunction(first_region,second_region){var overlap=3Dcompute_overlap= (first_region,second_region);return(overlap!=3D=3DBEFORE&&overlap!=3D=3DAFT= ER)};var dashedLine=3Dfunction(ctx,x1,y1,x2,y2,dashLen){if(dashLen=3D=3D=3D= undefined){dashLen=3D4}var dX=3Dx2-x1;var dY=3Dy2-y1;var dashes=3DMath.floo= r(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=3DdX/dashes;var dashY=3DdY/dash= es;var q;for(q=3D0;q<dashes;q++,x1+=3DdashX,y1+=3DdashY){if(q%2!=3D=3D0){co= ntinue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle= =3Dfunction(ctx,down_vertex_x,down_vertex_y,side_len){var x1=3Ddown_vertex_= x-side_len/2,x2=3Ddown_vertex_x+side_len/2,y=3Ddown_vertex_y-Math.sqrt(side= _len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down= _vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=3Dthis.fillStyle;= ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=3Dfunction(default_val)= {this.default_val=3D(default_val?default_val:1)};Scaler.prototype.gen_val= =3Dfunction(input){return this.default_val};var Painter=3Dfunction(data,vie= w_start,view_end,prefs,mode){this.data=3Ddata;this.view_start=3Dview_start;= this.view_end=3Dview_end;this.prefs=3Dextend({},this.default_prefs,prefs);t= his.mode=3Dmode};Painter.prototype.default_prefs=3D{};Painter.prototype.dra= w=3Dfunction(ctx,width,height,w_scale){};var SummaryTreePainter=3Dfunction(= data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view= _end,prefs,mode)};SummaryTreePainter.prototype.default_prefs=3D{show_counts= :false};SummaryTreePainter.prototype.draw=3Dfunction(ctx,width,height,w_sca= le){var view_start=3Dthis.view_start,points=3Dthis.data.data,max=3D(this.pr= efs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=3Dheight;d= elta_x_px=3DMath.ceil(this.data.delta*w_scale);ctx.save();for(var i=3D0,len= =3Dpoints.length;i<len;i++){var x=3DMath.floor((points[i][0]-view_start)*w_= scale);var y=3Dpoints[i][1];if(!y){continue}var y_px=3Dy/max*height;if(y!= =3D=3D0&&y_px<1){y_px=3D1}ctx.fillStyle=3Dthis.prefs.block_color;ctx.fillRe= ct(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=3D4;if(this.prefs.= show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.= fillStyle=3Dthis.prefs.label_color;ctx.textAlign=3D"center";ctx.fillText(y,= x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][1])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][1])}this.= prefs.max_value=3Dmax_value}};LinePainter.prototype.default_prefs=3D{min_va= lue:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_co= lor:"#F66"};LinePainter.prototype.draw=3Dfunction(ctx,width,height,w_scale)= {var in_path=3Dfalse,min_value=3Dthis.prefs.min_value,max_value=3Dthis.pref= s.max_value,vertical_range=3Dmax_value-min_value,height_px=3Dheight,view_st= art=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data;ctx.save();var y_ze= ro=3DMath.round(height+min_value/vertical_range*height);if(mode!=3D=3D"Inte= nsity"){ctx.fillStyle=3D"#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath= ();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=3DMath.ceil((data= [1][0]-data[0][0])*w_scale)}else{delta_x_px=3D10}var pref_color=3DparseInt(= this.prefs.color.slice(1),16),pref_r=3D(pref_color&16711680)>>16,pref_g=3D(= pref_color&65280)>>8,pref_b=3Dpref_color&255;for(var i=3D0,len=3Ddata.lengt= h;i<len;i++){ctx.fillStyle=3Dctx.strokeStyle=3Dthis.prefs.color;x_scaled=3D= Math.round((data[i][0]-view_start-1)*w_scale);y=3Ddata[i][1];var top_overfl= ow=3Dfalse,bot_overflow=3Dfalse;if(y=3D=3D=3Dnull){if(in_path&&mode=3D=3D= =3D"Filled"){ctx.lineTo(x_scaled,height_px)}in_path=3Dfalse;continue}if(y<m= in_value){bot_overflow=3Dtrue;y=3Dmin_value}else{if(y>max_value){top_overfl= ow=3Dtrue;y=3Dmax_value}}if(mode=3D=3D=3D"Histogram"){y=3DMath.round(y/vert= ical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(m= ode=3D=3D=3D"Intensity"){var saturation=3D(y-min_value)/vertical_range,new_= r=3DMath.round(pref_r+(255-pref_r)*(1-saturation)),new_g=3DMath.round(pref_= g+(255-pref_g)*(1-saturation)),new_b=3DMath.round(pref_b+(255-pref_b)*(1-sa= turation));ctx.fillStyle=3D"rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRec= t(x_scaled,0,delta_x_px,height_px)}else{y=3DMath.round(height_px-(y-min_val= ue)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_pa= th=3Dtrue;if(mode=3D=3D=3D"Filled"){ctx.moveTo(x_scaled,height_px);ctx.line= To(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=3Dthis.prefs.ov= erflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode=3D=3D=3D= "Histogram"||mode=3D=3D=3D"Intensity"){overflow_x=3Ddelta_x_px}else{x_scale= d-=3D2;overflow_x=3D4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3= )}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fil= lStyle=3Dthis.prefs.color}if(mode=3D=3D=3D"Filled"){if(in_path){ctx.lineTo(= x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.rest= ore()};var FeaturePositionMapper=3Dfunction(slot_height){this.feature_posit= ions=3D{};this.slot_height=3Dslot_height;this.translation=3D0;this.y_transl= ation=3D0};FeaturePositionMapper.prototype.map_feature_data=3Dfunction(feat= ure_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature= _positions[slot]=3D[]}this.feature_positions[slot].push({data:feature_data,= x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_= data=3Dfunction(x,y){var slot=3DMath.floor((y-this.y_translation)/this.slot= _height),feature_dict;if(!this.feature_positions[slot]){return null}x+=3Dth= is.translation;for(var i=3D0;i<this.feature_positions[slot].length;i++){fea= ture_dict=3Dthis.feature_positions[slot][i];if(x>=3Dfeature_dict.x_start&&x= <=3Dfeature_dict.x_end){return feature_dict.data}}};var FeaturePainter=3Dfu= nction(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Pain= ter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=3D(alp= ha_scaler?alpha_scaler:new Scaler());this.height_scaler=3D(height_scaler?he= ight_scaler:new Scaler())};FeaturePainter.prototype.default_prefs=3D{block_= color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_r= equired_height:function(rows_required,width){var required_height=3Dthis.get= _row_height(),y_scale=3Drequired_height,mode=3Dthis.mode;if(mode=3D=3D=3D"n= o_detail"||mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Pack"){required_height=3Dro= ws_required*y_scale}return required_height+this.get_top_padding(width)+this= .get_bottom_padding(width)},get_top_padding:function(width){return 0},get_b= ottom_padding:function(width){return Math.max(Math.round(this.get_row_heigh= t()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=3Dthis.da= ta,view_start=3Dthis.view_start,view_end=3Dthis.view_end;ctx.save();ctx.fil= lStyle=3Dthis.prefs.block_color;ctx.textAlign=3D"right";var y_scale=3Dthis.= get_row_height(),feature_mapper=3Dnew FeaturePositionMapper(y_scale),x_draw= _coords;for(var i=3D0,len=3Ddata.length;i<len;i++){var feature=3Ddata[i],fe= ature_uid=3Dfeature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],= slot=3D(slots&&slots[feature_uid]!=3D=3Dundefined?slots[feature_uid]:null);= if((feature_start<view_end&&feature_end>view_start)&&(this.mode=3D=3D=3D"De= nse"||slot!=3D=3Dnull)){x_draw_coords=3Dthis.draw_element(ctx,this.mode,fea= ture,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_fea= ture_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();fe= ature_mapper.y_translation=3Dthis.get_top_padding(width);return feature_map= per},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale= ,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]= }});var DENSE_TRACK_HEIGHT=3D10,NO_DETAIL_TRACK_HEIGHT=3D3,SQUISH_TRACK_HEI= GHT=3D5,PACK_TRACK_HEIGHT=3D10,NO_DETAIL_FEATURE_HEIGHT=3D1,DENSE_FEATURE_H= EIGHT=3D9,SQUISH_FEATURE_HEIGHT=3D3,PACK_FEATURE_HEIGHT=3D9,LABEL_SPACING= =3D2,CONNECTOR_COLOR=3D"#ccc";var LinkedFeaturePainter=3Dfunction(data,view= _start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(= this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.d= raw_background_connector=3Dtrue;this.draw_individual_connectors=3Dfalse};ex= tend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_heigh= t:function(){var mode=3Dthis.mode,height;if(mode=3D=3D=3D"Dense"){height=3D= DENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"no_detail"){height=3DNO_DETAIL_TRA= CK_HEIGHT}else{if(mode=3D=3D=3D"Squish"){height=3DSQUISH_TRACK_HEIGHT}else{= height=3DPACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,= feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfe= ature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2]-1,feature_name= =3Dfeature[3],feature_strand=3Dfeature[4],f_start=3DMath.floor(Math.max(0,(= feature_start-tile_low)*w_scale)),f_end=3DMath.ceil(Math.min(width,Math.max= (0,(feature_end-tile_low)*w_scale))),draw_start=3Df_start,draw_end=3Df_end,= y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale+this.get_top_padding(w= idth),thickness,y_start,thick_start=3Dnull,thick_end=3Dnull,block_color=3D(= !feature_strand||feature_strand=3D=3D=3D"+"||feature_strand=3D=3D=3D"."?thi= s.prefs.block_color:this.prefs.reverse_strand_color);label_color=3Dthis.pre= fs.label_color;ctx.globalAlpha=3Dthis.alpha_scaler.gen_val(feature);if(mode= =3D=3D=3D"Dense"){slot=3D1}if(mode=3D=3D=3D"no_detail"){ctx.fillStyle=3Dblo= ck_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HE= IGHT)}else{var feature_ts=3Dfeature[5],feature_te=3Dfeature[6],feature_bloc= ks=3Dfeature[7],full_height=3Dtrue;if(feature_ts&&feature_te){thick_start= =3DMath.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=3DMath.c= eil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_hei= ght,thick_height;if(mode=3D=3D=3D"Squish"){thin_height=3D1;thick_height=3DS= QUISH_FEATURE_HEIGHT;full_height=3Dfalse}else{if(mode=3D=3D=3D"Dense"){thin= _height=3D5;thick_height=3DDENSE_FEATURE_HEIGHT}else{thin_height=3D5;thick_= height=3DPACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=3Dblock_col= or;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_s= trand&&full_height){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canv= as.manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"= -"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.= fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_cen= ter,cur_height;if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){cur_y_center= =3Dy_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}else{if(fe= ature_strand){cur_y_center=3Dy_center;cur_height=3Dthick_height}else{cur_y_= center+=3D(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}}if(this.draw_backgrou= nd_connector){if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){ctx.fillStyle= =3DCONNECTOR_COLOR}else{if(feature_strand){if(feature_strand=3D=3D=3D"+"){c= tx.fillStyle=3Dctx.canvas.manager.get_pattern("right_strand")}else{if(featu= re_strand=3D=3D=3D"-"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left= _strand")}}}else{ctx.fillStyle=3DCONNECTOR_COLOR}}ctx.fillRect(f_start,cur_= y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=3D0,k_len= =3Dfeature_blocks.length;k<k_len;k++){var block=3Dfeature_blocks[k],block_s= tart=3DMath.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=3DMath= .ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_s= tart,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=3Dbloc= k_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,bl= ock_end-block_start,thin_height);if(thick_start!=3D=3Dundefined&&feature_te= >feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thi= ck_start=3DMath.max(block_start,thick_start),block_thick_end=3DMath.min(blo= ck_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end= -block_thick_start,thick_height);if(feature_blocks.length=3D=3D=3D1&&mode= =3D=3D=3D"Pack"){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canvas.= manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"-")= {ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}if(bloc= k_thick_start+14<block_thick_end){block_thick_start+=3D2;block_thick_end-= =3D2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_= start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){= this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_e= nd,y_center)}last_block_start=3Dblock_start;last_block_end=3Dblock_end}if(m= ode=3D=3D=3D"Pack"){ctx.globalAlpha=3D1;ctx.fillStyle=3D"white";var hscale_= factor=3Dthis.height_scaler.gen_val(feature),new_height=3DMath.ceil(thick_h= eight*hscale_factor),ws_height=3DMath.round((thick_height-new_height)/2);if= (hscale_factor!=3D=3D1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,w= s_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-= f_start,ws_height)}}}ctx.globalAlpha=3D1;if(feature_name&&mode=3D=3D=3D"Pac= k"&&feature_start>tile_low){ctx.fillStyle=3Dlabel_color;if(tile_low=3D=3D= =3D0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign=3D"left"= ;ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=3Dctx.= measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign=3D"right";= ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=3Dc= tx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=3D1;retu= rn[draw_start,draw_end]}});var ReadPainter=3Dfunction(data,view_start,view_= end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this= ,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_s= eq=3D(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePaint= er.prototype,{get_row_height:function(){var height,mode=3Dthis.mode;if(mode= =3D=3D=3D"Dense"){height=3DDENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"Squish"= ){height=3DSQUISH_TRACK_HEIGHT}else{height=3DPACK_TRACK_HEIGHT;if(this.pref= s.show_insertions){height*=3D2}}}return height},draw_read:function(ctx,mode= ,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ct= x.textAlign=3D"center";var tile_region=3D[tile_low,tile_high],base_offset= =3D0,seq_offset=3D0,gap=3D0,char_width_px=3Dctx.canvas.manager.char_width_p= x,block_color=3D(strand=3D=3D=3D"+"?this.prefs.block_color:this.prefs.rever= se_strand_color);var draw_last=3D[];if((mode=3D=3D=3D"Pack"||this.mode=3D= =3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){gap=3DMath.r= ound(w_scale/2)}if(!cigar){cigar=3D[[0,ref_seq.length]]}for(var cig_id=3D0,= len=3Dcigar.length;cig_id<len;cig_id++){var cig=3Dcigar[cig_id],cig_op=3D"M= IDNSHP=3DX"[cig[0]],cig_len=3Dcig[1];if(cig_op=3D=3D=3D"H"||cig_op=3D=3D=3D= "S"){base_offset-=3Dcig_len}var seq_start=3D(feature_start-1)+base_offset,s= _start=3DMath.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=3DMath.= floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start=3D=3D=3D= s_end){s_end+=3D1}switch(cig_op){case"H":break;case"S":case"M":case"=3D":if= (is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=3Dref_seq.s= lice(seq_offset-1,seq_offset+cig_len);if(gap>0){ctx.fillStyle=3Dblock_color= ;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=3DCONNE= CTOR_COLOR;for(var c=3D0,str_len=3Dseq.length;c<str_len;c++){if(this.prefs.= show_differences){if(this.ref_seq){var ref_char=3Dthis.ref_seq[seq_start-ti= le_low+c];if(!ref_char||ref_char.toLowerCase()=3D=3D=3Dseq[c].toLowerCase()= ){continue}}else{continue}}if(seq_start+c>=3Dtile_low&&seq_start+c<=3Dtile_= high){var c_start=3DMath.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));= ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=3Dblock_color;= ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_o= ffset+=3Dcig_len;base_offset+=3Dcig_len;break;case"N":ctx.fillStyle=3DCONNE= CTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset= +=3Dcig_len;break;case"D":ctx.fillStyle=3D"red";ctx.fillRect(s_start-gap,y_= center+4,s_end-s_start,3);base_offset+=3Dcig_len;break;case"P":break;case"I= ":var insert_x_coord=3Ds_start-gap;if(is_overlap([seq_start,seq_start+cig_l= en],tile_region)){var seq=3Dref_seq.slice(seq_offset-1,seq_offset+cig_len);= if(this.prefs.show_insertions){var x_center=3Ds_start-(s_end-s_start)/2;if(= (mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w= _scale>char_width_px){ctx.fillStyle=3D"yellow";ctx.fillRect(x_center-gap,y_= center-9,s_end-s_start,9);draw_last[draw_last.length]=3D{type:"triangle",da= ta:[insert_x_coord,y_center+4,5]};ctx.fillStyle=3DCONNECTOR_COLOR;switch(co= mpute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_STA= RT):seq=3Dseq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=3Dseq.= slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS= ):seq=3Dseq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c= =3D0,str_len=3Dseq.length;c<str_len;c++){var c_start=3DMath.floor(Math.max(= 0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_sta= rt)/2,y_center)}}else{ctx.fillStyle=3D"yellow";ctx.fillRect(x_center,y_cent= er+(this.mode!=3D=3D"Dense"?2:5),s_end-s_start,(mode!=3D=3D"Dense"?SQUISH_F= EATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode=3D=3D=3D"Pack"||this.mo= de=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){draw_la= st.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}= seq_offset+=3Dcig_len;break;case"X":seq_offset+=3Dcig_len;break}}ctx.fillSt= yle=3D"yellow";var item,type,data;for(var i=3D0;i<draw_last.length;i++){ite= m=3Ddraw_last[i];type=3Ditem.type;data=3Ditem.data;if(type=3D=3D=3D"text"){= ctx.save();ctx.font=3D"bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]= );ctx.restore()}else{if(type=3D=3D=3D"triangle"){drawDownwardEquilateralTri= angle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,featu= re,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfeature= [0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],feature_name=3Dfeat= ure[3],f_start=3DMath.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f= _end=3DMath.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))= ),y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale,label_color=3Dthis.p= refs.label_color,gap=3D0;if((mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")= &&w_scale>ctx.canvas.manager.char_width_px){var gap=3DMath.round(w_scale/2)= }if(feature[5] instanceof Array){var b1_start=3DMath.floor(Math.max(0,(feat= ure[4][0]-tile_low)*w_scale)),b1_end=3DMath.ceil(Math.min(width,Math.max(0,= (feature[4][1]-tile_low)*w_scale))),b2_start=3DMath.floor(Math.max(0,(featu= re[5][0]-tile_low)*w_scale)),b2_end=3DMath.ceil(Math.min(width,Math.max(0,(= feature[5][1]-tile_low)*w_scale))),connector=3Dtrue;if(feature[4][1]>=3Dtil= e_low&&feature[4][0]<=3Dtile_high&&feature[4][2]){this.draw_read(ctx,mode,w= _scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3= ],feature[4][4])}else{connector=3Dfalse}if(feature[5][1]>=3Dtile_low&&featu= re[5][0]<=3Dtile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_cen= ter,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5]= [4])}else{connector=3Dfalse}if(connector&&b2_start>b1_end){ctx.fillStyle=3D= CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+= 5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,featur= e_start,feature[4],feature[5],feature[6])}if(mode=3D=3D=3D"Pack"&&feature_s= tart>tile_low&&feature_name!=3D=3D"."){ctx.fillStyle=3Dthis.prefs.label_col= or;var tile_index=3D1;if(tile_index=3D=3D=3D0&&f_start-ctx.measureText(feat= ure_name).width<0){ctx.textAlign=3D"left";ctx.fillText(feature_name,f_end+L= ABEL_SPACING-gap,y_center+8)}else{ctx.textAlign=3D"right";ctx.fillText(feat= ure_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinke= dFeaturePainter=3Dfunction(data,view_start,view_end,prefs,mode,alpha_scaler= ,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,pre= fs,mode,alpha_scaler,height_scaler);this.longest_feature_length=3Dthis.calc= ulate_longest_feature_length();this.draw_background_connector=3Dfalse;this.= draw_individual_connectors=3Dtrue};extend(ArcLinkedFeaturePainter.prototype= ,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest= _feature_length:function(){var longest_feature_length=3D0;for(var i=3D0,len= =3Dthis.data.length;i<len;i++){var feature=3Dthis.data[i],feature_start=3Df= eature[1],feature_end=3Dfeature[2];longest_feature_length=3DMath.max(longes= t_feature_length,feature_end-feature_start)}return longest_feature_length},= get_top_padding:function(width){var view_range=3Dthis.view_end-this.view_st= art,w_scale=3Dwidth/view_range;return Math.min(128,Math.ceil((this.longest_= feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block= 1_end,block2_start,block2_end,y_center){var x_center=3D(block1_end+block2_s= tart)/2,radius=3Dblock2_start-x_center;var angle1=3DMath.PI,angle2=3D0;if(r= adius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Ma= th.PI,0);ctx.stroke()}}});var Color=3Dfunction(rgb,a){if(Array.isArray(rgb)= ){this.rgb=3Drgb}else{if(rgb.length=3D=3D6){this.rgb=3Drgb.match(/.{2}/g).m= ap(function(c){return parseInt(c,16)})}else{this.rgb=3Drgb.split("").map(fu= nction(c){return parseInt(c+c,16)})}}this.alpha=3Dtypeof(a)=3D=3D=3D"number= "?a:1};Color.prototype=3D{eval:function(){return this},toCSS:function(){if(= this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)})= .concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){= i=3DMath.round(i);i=3D(i>255?255:(i<0?0:i)).toString(16);return i.length=3D= =3D=3D1?"0"+i:i}).join("")}},toHSL:function(){var r=3Dthis.rgb[0]/255,g=3Dt= his.rgb[1]/255,b=3Dthis.rgb[2]/255,a=3Dthis.alpha;var max=3DMath.max(r,g,b)= ,min=3DMath.min(r,g,b);var h,s,l=3D(max+min)/2,d=3Dmax-min;if(max=3D=3D=3Dm= in){h=3Ds=3D0}else{s=3Dl>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h= =3D(g-b)/d+(g<b?6:0);break;case g:h=3D(b-r)/d+2;break;case b:h=3D(r-g)/d+4;= break}h/=3D6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=3D[Mat= h.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i= =3DMath.round(i);i=3D(i>255?255:(i<0?0:i)).toString(16);return i.length=3D= =3D=3D1?"0"+i:i}).join("")},mix:function(color2,weight){color1=3Dthis;var p= =3Dweight;var w=3Dp*2-1;var a=3Dcolor1.toHSL().a-color2.toHSL().a;var w1=3D= (((w*a=3D=3D-1)?w:(w+a)/(1+w*a))+1)/2;var w2=3D1-w1;var rgb=3D[color1.rgb[0= ]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+co= lor2.rgb[2]*w2];var alpha=3Dcolor1.alpha*p+color2.alpha*(1-p);return new Co= lor(rgb,alpha)}};var LinearRamp=3Dfunction(start_color,end_color,start_valu= e,end_value){this.start_color=3Dnew Color(start_color);this.end_color=3Dnew= Color(end_color);this.start_value=3Dstart_value;this.end_value=3Dend_value= ;this.value_range=3Dend_value-start_value};LinearRamp.prototype.map_value= =3Dfunction(value){value=3DMath.max(value,this.start_value);value=3DMath.mi= n(value,this.end_value);value=3D(value-this.start_value)/this.value_range;r= eturn this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp= =3Dfunction(start_color,middle_color,end_color,start_value,end_value){this.= positive_ramp=3Dnew LinearRamp(middle_color,end_color,0,end_value);this.neg= ative_ramp=3Dnew LinearRamp(middle_color,start_color,0,-start_value);this.s= tart_value=3Dstart_value;this.end_value=3Dend_value};SplitRamp.prototype.ma= p_value=3Dfunction(value){value=3DMath.max(value,this.start_value);value=3D= Math.min(value,this.end_value);if(value>=3D0){return this.positive_ramp.map= _value(value)}else{return this.negative_ramp.map_value(-value)}};var Diagon= alHeatmapPainter=3Dfunction(data,view_start,view_end,prefs,mode){Painter.ca= ll(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_va= lue=3D=3D=3Dundefined){var min_value=3DInfinity;for(i=3D0,len=3Dthis.data.l= ength;i<len;i++){min_value=3DMath.min(min_value,this.data[i][5])}this.prefs= .min_value=3Dmin_value}if(this.prefs.max_value=3D=3D=3Dundefined){var max_v= alue=3D-Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){max_value=3DMa= th.max(max_value,this.data[i][5])}this.prefs.max_value=3Dmax_value}};Diagon= alHeatmapPainter.prototype.default_prefs=3D{min_value:undefined,max_value:u= ndefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHe= atmapPainter.prototype.draw=3Dfunction(ctx,width,height,w_scale){var min_va= lue=3Dthis.prefs.min_value,max_value=3Dthis.prefs.max_value,value_range=3Dm= ax_value-min_value,height_px=3Dheight,view_start=3Dthis.view_start,mode=3Dt= his.mode,data=3Dthis.data,invsqrt2=3D1/Math.sqrt(2);var ramp=3D(new SplitRa= mp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value))= ;var d,s1,e1,s2,e2,value;var scale=3Dfunction(p){return(p-view_start)*w_sca= le};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for= (var i=3D0,len=3Ddata.length;i<len;i++){d=3Ddata[i];s1=3Dscale(d[1]);e1=3Ds= cale(d[2]);s2=3Dscale(d[4]);e2=3Dscale(d[5]);value=3Dd[6];ctx.fillStyle=3D(= ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};r= eturn{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LineP= ainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,Ar= cLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:Diagon= alHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=3D_.extend;var BEFORE=3D= 1001,CONTAINS=3D1002,OVERLAP_START=3D1003,OVERLAP_END=3D1004,CONTAINED_BY= =3D1005,AFTER=3D1006;var compute_overlap=3Dfunction(first_region,second_reg= ion){var first_start=3Dfirst_region[0],first_end=3Dfirst_region[1],second_s= tart=3Dsecond_region[0],second_end=3Dsecond_region[1],overlap;if(first_star= t<second_start){if(first_end<second_start){overlap=3DBEFORE}else{if(first_e= nd<=3Dsecond_end){overlap=3DOVERLAP_START}else{overlap=3DCONTAINS}}}else{if= (first_start>second_end){overlap=3DAFTER}else{if(first_end<=3Dsecond_end){o= verlap=3DCONTAINED_BY}else{overlap=3DOVERLAP_END}}}return overlap};var is_o= verlap=3Dfunction(first_region,second_region){var overlap=3Dcompute_overlap= (first_region,second_region);return(overlap!=3D=3DBEFORE&&overlap!=3D=3DAFT= ER)};var dashedLine=3Dfunction(ctx,x1,y1,x2,y2,dashLen){if(dashLen=3D=3D=3D= undefined){dashLen=3D4}var dX=3Dx2-x1;var dY=3Dy2-y1;var dashes=3DMath.floo= r(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=3DdX/dashes;var dashY=3DdY/dash= es;var q;for(q=3D0;q<dashes;q++,x1+=3DdashX,y1+=3DdashY){if(q%2!=3D=3D0){co= ntinue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle= =3Dfunction(ctx,down_vertex_x,down_vertex_y,side_len){var x1=3Ddown_vertex_= x-side_len/2,x2=3Ddown_vertex_x+side_len/2,y=3Ddown_vertex_y-Math.sqrt(side= _len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down= _vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=3Dthis.fillStyle;= ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=3Dfunction(default_val)= {this.default_val=3D(default_val?default_val:1)};Scaler.prototype.gen_val= =3Dfunction(input){return this.default_val};var Painter=3Dfunction(data,vie= w_start,view_end,prefs,mode){this.data=3Ddata;this.view_start=3Dview_start;= this.view_end=3Dview_end;this.prefs=3Dextend({},this.default_prefs,prefs);t= his.mode=3Dmode};Painter.prototype.default_prefs=3D{};Painter.prototype.dra= w=3Dfunction(ctx,width,height,w_scale){};var SummaryTreePainter=3Dfunction(= data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view= _end,prefs,mode)};SummaryTreePainter.prototype.default_prefs=3D{show_counts= :false};SummaryTreePainter.prototype.draw=3Dfunction(ctx,width,height,w_sca= le){var view_start=3Dthis.view_start,points=3Dthis.data.data,max=3D(this.pr= efs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=3Dheight;d= elta_x_px=3DMath.ceil(this.data.delta*w_scale);ctx.save();for(var i=3D0,len= =3Dpoints.length;i<len;i++){var x=3DMath.floor((points[i][0]-view_start)*w_= scale);var y=3Dpoints[i][1];if(!y){continue}var y_px=3Dy/max*height;if(y!= =3D=3D0&&y_px<1){y_px=3D1}ctx.fillStyle=3Dthis.prefs.block_color;ctx.fillRe= ct(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=3D4;if(this.prefs.= show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.= fillStyle=3Dthis.prefs.label_color;ctx.textAlign=3D"center";ctx.fillText(y,= x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][1])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][1])}this.= prefs.max_value=3Dmax_value}};LinePainter.prototype.default_prefs=3D{min_va= lue:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_co= lor:"#F66"};LinePainter.prototype.draw=3Dfunction(ctx,width,height,w_scale)= {var in_path=3Dfalse,min_value=3Dthis.prefs.min_value,max_value=3Dthis.pref= s.max_value,vertical_range=3Dmax_value-min_value,height_px=3Dheight,view_st= art=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data;ctx.save();var y_ze= ro=3DMath.round(height+min_value/vertical_range*height);if(mode!=3D=3D"Inte= nsity"){ctx.fillStyle=3D"#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath= ();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=3DMath.ceil((data= [1][0]-data[0][0])*w_scale)}else{delta_x_px=3D10}var pref_color=3DparseInt(= this.prefs.color.slice(1),16),pref_r=3D(pref_color&16711680)>>16,pref_g=3D(= pref_color&65280)>>8,pref_b=3Dpref_color&255;for(var i=3D0,len=3Ddata.lengt= h;i<len;i++){ctx.fillStyle=3Dctx.strokeStyle=3Dthis.prefs.color;x_scaled=3D= Math.round((data[i][0]-view_start-1)*w_scale);y=3Ddata[i][1];var top_overfl= ow=3Dfalse,bot_overflow=3Dfalse;if(y=3D=3D=3Dnull){if(in_path&&mode=3D=3D= =3D"Filled"){ctx.lineTo(x_scaled,height_px)}in_path=3Dfalse;continue}if(y<m= in_value){bot_overflow=3Dtrue;y=3Dmin_value}else{if(y>max_value){top_overfl= ow=3Dtrue;y=3Dmax_value}}if(mode=3D=3D=3D"Histogram"){y=3DMath.round(y/vert= ical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(m= ode=3D=3D=3D"Intensity"){var saturation=3D(y-min_value)/vertical_range,new_= r=3DMath.round(pref_r+(255-pref_r)*(1-saturation)),new_g=3DMath.round(pref_= g+(255-pref_g)*(1-saturation)),new_b=3DMath.round(pref_b+(255-pref_b)*(1-sa= turation));ctx.fillStyle=3D"rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRec= t(x_scaled,0,delta_x_px,height_px)}else{y=3DMath.round(height_px-(y-min_val= ue)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_pa= th=3Dtrue;if(mode=3D=3D=3D"Filled"){ctx.moveTo(x_scaled,height_px);ctx.line= To(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=3Dthis.prefs.ov= erflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode=3D=3D=3D= "Histogram"||mode=3D=3D=3D"Intensity"){overflow_x=3Ddelta_x_px}else{x_scale= d-=3D2;overflow_x=3D4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3= )}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fil= lStyle=3Dthis.prefs.color}if(mode=3D=3D=3D"Filled"){if(in_path){ctx.lineTo(= x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.rest= ore()};var FeaturePositionMapper=3Dfunction(slot_height){this.feature_posit= ions=3D{};this.slot_height=3Dslot_height;this.translation=3D0;this.y_transl= ation=3D0};FeaturePositionMapper.prototype.map_feature_data=3Dfunction(feat= ure_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature= _positions[slot]=3D[]}this.feature_positions[slot].push({data:feature_data,= x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_= data=3Dfunction(x,y){var slot=3DMath.floor((y-this.y_translation)/this.slot= _height),feature_dict;if(!this.feature_positions[slot]){return null}x+=3Dth= is.translation;for(var i=3D0;i<this.feature_positions[slot].length;i++){fea= ture_dict=3Dthis.feature_positions[slot][i];if(x>=3Dfeature_dict.x_start&&x= <=3Dfeature_dict.x_end){return feature_dict.data}}};var FeaturePainter=3Dfu= nction(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Pain= ter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=3D(alp= ha_scaler?alpha_scaler:new Scaler());this.height_scaler=3D(height_scaler?he= ight_scaler:new Scaler())};FeaturePainter.prototype.default_prefs=3D{block_= color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_r= equired_height:function(rows_required,width){var required_height=3Dthis.get= _row_height(),y_scale=3Drequired_height,mode=3Dthis.mode;if(mode=3D=3D=3D"n= o_detail"||mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Pack"){required_height=3Dro= ws_required*y_scale}return required_height+this.get_top_padding(width)+this= .get_bottom_padding(width)},get_top_padding:function(width){return 0},get_b= ottom_padding:function(width){return Math.max(Math.round(this.get_row_heigh= t()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=3Dthis.da= ta,view_start=3Dthis.view_start,view_end=3Dthis.view_end;ctx.save();ctx.fil= lStyle=3Dthis.prefs.block_color;ctx.textAlign=3D"right";var y_scale=3Dthis.= get_row_height(),feature_mapper=3Dnew FeaturePositionMapper(y_scale),x_draw= _coords;for(var i=3D0,len=3Ddata.length;i<len;i++){var feature=3Ddata[i],fe= ature_uid=3Dfeature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],= slot=3D(slots&&slots[feature_uid]!=3D=3Dundefined?slots[feature_uid]:null);= if((feature_start<view_end&&feature_end>view_start)&&(this.mode=3D=3D=3D"De= nse"||slot!=3D=3Dnull)){x_draw_coords=3Dthis.draw_element(ctx,this.mode,fea= ture,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_fea= ture_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();fe= ature_mapper.y_translation=3Dthis.get_top_padding(width);return feature_map= per},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale= ,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]= }});var DENSE_TRACK_HEIGHT=3D10,NO_DETAIL_TRACK_HEIGHT=3D3,SQUISH_TRACK_HEI= GHT=3D5,PACK_TRACK_HEIGHT=3D10,NO_DETAIL_FEATURE_HEIGHT=3D1,DENSE_FEATURE_H= EIGHT=3D9,SQUISH_FEATURE_HEIGHT=3D3,PACK_FEATURE_HEIGHT=3D9,LABEL_SPACING= =3D2,CONNECTOR_COLOR=3D"#ccc";var LinkedFeaturePainter=3Dfunction(data,view= _start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(= this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.d= raw_background_connector=3Dtrue;this.draw_individual_connectors=3Dfalse};ex= tend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_heigh= t:function(){var mode=3Dthis.mode,height;if(mode=3D=3D=3D"Dense"){height=3D= DENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"no_detail"){height=3DNO_DETAIL_TRA= CK_HEIGHT}else{if(mode=3D=3D=3D"Squish"){height=3DSQUISH_TRACK_HEIGHT}else{= height=3DPACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,= feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfe= ature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2]-1,feature_name= =3Dfeature[3],feature_strand=3Dfeature[4],f_start=3DMath.floor(Math.max(0,(= feature_start-tile_low)*w_scale)),f_end=3DMath.ceil(Math.min(width,Math.max= (0,(feature_end-tile_low)*w_scale))),draw_start=3Df_start,draw_end=3Df_end,= y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale+this.get_top_padding(w= idth),thickness,y_start,thick_start=3Dnull,thick_end=3Dnull,block_color=3D(= !feature_strand||feature_strand=3D=3D=3D"+"||feature_strand=3D=3D=3D"."?thi= s.prefs.block_color:this.prefs.reverse_strand_color);label_color=3Dthis.pre= fs.label_color;ctx.globalAlpha=3Dthis.alpha_scaler.gen_val(feature);if(mode= =3D=3D=3D"Dense"){slot=3D1}if(mode=3D=3D=3D"no_detail"){ctx.fillStyle=3Dblo= ck_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HE= IGHT)}else{var feature_ts=3Dfeature[5],feature_te=3Dfeature[6],feature_bloc= ks=3Dfeature[7],full_height=3Dtrue;if(feature_ts&&feature_te){thick_start= =3DMath.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=3DMath.c= eil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_hei= ght,thick_height;if(mode=3D=3D=3D"Squish"){thin_height=3D1;thick_height=3DS= QUISH_FEATURE_HEIGHT;full_height=3Dfalse}else{if(mode=3D=3D=3D"Dense"){thin= _height=3D5;thick_height=3DDENSE_FEATURE_HEIGHT}else{thin_height=3D5;thick_= height=3DPACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=3Dblock_col= or;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_s= trand&&full_height){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canv= as.manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"= -"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.= fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_cen= ter,cur_height;if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){cur_y_center= =3Dy_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}else{if(fe= ature_strand){cur_y_center=3Dy_center;cur_height=3Dthick_height}else{cur_y_= center+=3D(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}}if(this.draw_backgrou= nd_connector){if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){ctx.fillStyle= =3DCONNECTOR_COLOR}else{if(feature_strand){if(feature_strand=3D=3D=3D"+"){c= tx.fillStyle=3Dctx.canvas.manager.get_pattern("right_strand")}else{if(featu= re_strand=3D=3D=3D"-"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left= _strand")}}}else{ctx.fillStyle=3DCONNECTOR_COLOR}}ctx.fillRect(f_start,cur_= y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=3D0,k_len= =3Dfeature_blocks.length;k<k_len;k++){var block=3Dfeature_blocks[k],block_s= tart=3DMath.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=3DMath= .ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_s= tart,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=3Dbloc= k_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,bl= ock_end-block_start,thin_height);if(thick_start!=3D=3Dundefined&&feature_te= >feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thi= ck_start=3DMath.max(block_start,thick_start),block_thick_end=3DMath.min(blo= ck_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end= -block_thick_start,thick_height);if(feature_blocks.length=3D=3D=3D1&&mode= =3D=3D=3D"Pack"){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canvas.= manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"-")= {ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}if(bloc= k_thick_start+14<block_thick_end){block_thick_start+=3D2;block_thick_end-= =3D2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_= start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){= this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_e= nd,y_center)}last_block_start=3Dblock_start;last_block_end=3Dblock_end}if(m= ode=3D=3D=3D"Pack"){ctx.globalAlpha=3D1;ctx.fillStyle=3D"white";var hscale_= factor=3Dthis.height_scaler.gen_val(feature),new_height=3DMath.ceil(thick_h= eight*hscale_factor),ws_height=3DMath.round((thick_height-new_height)/2);if= (hscale_factor!=3D=3D1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,w= s_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-= f_start,ws_height)}}}ctx.globalAlpha=3D1;if(feature_name&&mode=3D=3D=3D"Pac= k"&&feature_start>tile_low){ctx.fillStyle=3Dlabel_color;if(tile_low=3D=3D= =3D0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign=3D"left"= ;ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=3Dctx.= measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign=3D"right";= ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=3Dc= tx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=3D1;retu= rn[draw_start,draw_end]}});var ReadPainter=3Dfunction(data,view_start,view_= end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this= ,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_s= eq=3D(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePaint= er.prototype,{get_row_height:function(){var height,mode=3Dthis.mode;if(mode= =3D=3D=3D"Dense"){height=3DDENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"Squish"= ){height=3DSQUISH_TRACK_HEIGHT}else{height=3DPACK_TRACK_HEIGHT;if(this.pref= s.show_insertions){height*=3D2}}}return height},draw_read:function(ctx,mode= ,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ct= x.textAlign=3D"center";var tile_region=3D[tile_low,tile_high],base_offset= =3D0,seq_offset=3D0,gap=3D0,char_width_px=3Dctx.canvas.manager.char_width_p= x,block_color=3D(strand=3D=3D=3D"+"?this.prefs.block_color:this.prefs.rever= se_strand_color);var draw_last=3D[];if((mode=3D=3D=3D"Pack"||this.mode=3D= =3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){gap=3DMath.r= ound(w_scale/2)}if(!cigar){cigar=3D[[0,ref_seq.length]]}for(var cig_id=3D0,= len=3Dcigar.length;cig_id<len;cig_id++){var cig=3Dcigar[cig_id],cig_op=3D"M= IDNSHP=3DX"[cig[0]],cig_len=3Dcig[1];if(cig_op=3D=3D=3D"H"||cig_op=3D=3D=3D= "S"){base_offset-=3Dcig_len}var seq_start=3D(feature_start-1)+base_offset,s= _start=3DMath.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=3DMath.= floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start=3D=3D=3D= s_end){s_end+=3D1}switch(cig_op){case"H":break;case"S":case"M":case"=3D":if= (is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=3Dref_seq.s= lice(seq_offset-1,seq_offset+cig_len);if(gap>0){ctx.fillStyle=3Dblock_color= ;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=3DCONNE= CTOR_COLOR;for(var c=3D0,str_len=3Dseq.length;c<str_len;c++){if(this.prefs.= show_differences){if(this.ref_seq){var ref_char=3Dthis.ref_seq[seq_start-ti= le_low+c];if(!ref_char||ref_char.toLowerCase()=3D=3D=3Dseq[c].toLowerCase()= ){continue}}else{continue}}if(seq_start+c>=3Dtile_low&&seq_start+c<=3Dtile_= high){var c_start=3DMath.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));= ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=3Dblock_color;= ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_o= ffset+=3Dcig_len;base_offset+=3Dcig_len;break;case"N":ctx.fillStyle=3DCONNE= CTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset= +=3Dcig_len;break;case"D":ctx.fillStyle=3D"red";ctx.fillRect(s_start-gap,y_= center+4,s_end-s_start,3);base_offset+=3Dcig_len;break;case"P":break;case"I= ":var insert_x_coord=3Ds_start-gap;if(is_overlap([seq_start,seq_start+cig_l= en],tile_region)){var seq=3Dref_seq.slice(seq_offset-1,seq_offset+cig_len);= if(this.prefs.show_insertions){var x_center=3Ds_start-(s_end-s_start)/2;if(= (mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w= _scale>char_width_px){ctx.fillStyle=3D"yellow";ctx.fillRect(x_center-gap,y_= center-9,s_end-s_start,9);draw_last[draw_last.length]=3D{type:"triangle",da= ta:[insert_x_coord,y_center+4,5]};ctx.fillStyle=3DCONNECTOR_COLOR;switch(co= mpute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_STA= RT):seq=3Dseq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=3Dseq.= slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS= ):seq=3Dseq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c= =3D0,str_len=3Dseq.length;c<str_len;c++){var c_start=3DMath.floor(Math.max(= 0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_sta= rt)/2,y_center)}}else{ctx.fillStyle=3D"yellow";ctx.fillRect(x_center,y_cent= er+(this.mode!=3D=3D"Dense"?2:5),s_end-s_start,(mode!=3D=3D"Dense"?SQUISH_F= EATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode=3D=3D=3D"Pack"||this.mo= de=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){draw_la= st.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}= seq_offset+=3Dcig_len;break;case"X":seq_offset+=3Dcig_len;break}}ctx.fillSt= yle=3D"yellow";var item,type,data;for(var i=3D0;i<draw_last.length;i++){ite= m=3Ddraw_last[i];type=3Ditem.type;data=3Ditem.data;if(type=3D=3D=3D"text"){= ctx.save();ctx.font=3D"bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]= );ctx.restore()}else{if(type=3D=3D=3D"triangle"){drawDownwardEquilateralTri= angle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,featu= re,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfeature= [0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],feature_name=3Dfeat= ure[3],f_start=3DMath.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f= _end=3DMath.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))= ),y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale,label_color=3Dthis.p= refs.label_color,gap=3D0;if((mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")= &&w_scale>ctx.canvas.manager.char_width_px){var gap=3DMath.round(w_scale/2)= }if(feature[5] instanceof Array){var b1_start=3DMath.floor(Math.max(0,(feat= ure[4][0]-tile_low)*w_scale)),b1_end=3DMath.ceil(Math.min(width,Math.max(0,= (feature[4][1]-tile_low)*w_scale))),b2_start=3DMath.floor(Math.max(0,(featu= re[5][0]-tile_low)*w_scale)),b2_end=3DMath.ceil(Math.min(width,Math.max(0,(= feature[5][1]-tile_low)*w_scale))),connector=3Dtrue;if(feature[4][1]>=3Dtil= e_low&&feature[4][0]<=3Dtile_high&&feature[4][2]){this.draw_read(ctx,mode,w= _scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3= ],feature[4][4])}else{connector=3Dfalse}if(feature[5][1]>=3Dtile_low&&featu= re[5][0]<=3Dtile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_cen= ter,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5]= [4])}else{connector=3Dfalse}if(connector&&b2_start>b1_end){ctx.fillStyle=3D= CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+= 5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,featur= e_start,feature[4],feature[5],feature[6])}if(mode=3D=3D=3D"Pack"&&feature_s= tart>tile_low&&feature_name!=3D=3D"."){ctx.fillStyle=3Dthis.prefs.label_col= or;var tile_index=3D1;if(tile_index=3D=3D=3D0&&f_start-ctx.measureText(feat= ure_name).width<0){ctx.textAlign=3D"left";ctx.fillText(feature_name,f_end+L= ABEL_SPACING-gap,y_center+8)}else{ctx.textAlign=3D"right";ctx.fillText(feat= ure_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinke= dFeaturePainter=3Dfunction(data,view_start,view_end,prefs,mode,alpha_scaler= ,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,pre= fs,mode,alpha_scaler,height_scaler);this.longest_feature_length=3Dthis.calc= ulate_longest_feature_length();this.draw_background_connector=3Dfalse;this.= draw_individual_connectors=3Dtrue};extend(ArcLinkedFeaturePainter.prototype= ,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest= _feature_length:function(){var longest_feature_length=3D0;for(var i=3D0,len= =3Dthis.data.length;i<len;i++){var feature=3Dthis.data[i],feature_start=3Df= eature[1],feature_end=3Dfeature[2];longest_feature_length=3DMath.max(longes= t_feature_length,feature_end-feature_start)}return longest_feature_length},= get_top_padding:function(width){var view_range=3Dthis.view_end-this.view_st= art,w_scale=3Dwidth/view_range;return Math.min(128,Math.ceil((this.longest_= feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block= 1_end,block2_start,block2_end,y_center){var x_center=3D(block1_end+block2_s= tart)/2,radius=3Dblock2_start-x_center;var angle1=3DMath.PI,angle2=3D0;if(r= adius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Ma= th.PI,0);ctx.stroke()}}});var Color=3Dfunction(rgb,a){if(Array.isArray(rgb)= ){this.rgb=3Drgb}else{if(rgb.length=3D=3D6){this.rgb=3Drgb.match(/.{2}/g).m= ap(function(c){return parseInt(c,16)})}else{if(rgb.length=3D=3D7){this.rgb= =3Drgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)}= )}else{this.rgb=3Drgb.split("").map(function(c){return parseInt(c+c,16)})}}= }this.alpha=3Dtypeof(a)=3D=3D=3D"number"?a:1};Color.prototype=3D{eval:funct= ion(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb= .map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}e= lse{return"#"+this.rgb.map(function(i){i=3DMath.round(i);i=3D(i>255?255:(i<= 0?0:i)).toString(16);return i.length=3D=3D=3D1?"0"+i:i}).join("")}},toHSL:f= unction(){var r=3Dthis.rgb[0]/255,g=3Dthis.rgb[1]/255,b=3Dthis.rgb[2]/255,a= =3Dthis.alpha;var max=3DMath.max(r,g,b),min=3DMath.min(r,g,b);var h,s,l=3D(= max+min)/2,d=3Dmax-min;if(max=3D=3D=3Dmin){h=3Ds=3D0}else{s=3Dl>0.5?d/(2-ma= x-min):d/(max+min);switch(max){case r:h=3D(g-b)/d+(g<b?6:0);break;case g:h= =3D(b-r)/d+2;break;case b:h=3D(r-g)/d+4;break}h/=3D6}return{h:h*360,s:s,l:l= ,a:a}},toARGB:function(){var argb=3D[Math.round(this.alpha*255)].concat(thi= s.rgb);return"#"+argb.map(function(i){i=3DMath.round(i);i=3D(i>255?255:(i<0= ?0:i)).toString(16);return i.length=3D=3D=3D1?"0"+i:i}).join("")},mix:funct= ion(color2,weight){color1=3Dthis;var p=3Dweight;var w=3Dp*2-1;var a=3Dcolor= 1.toHSL().a-color2.toHSL().a;var w1=3D(((w*a=3D=3D-1)?w:(w+a)/(1+w*a))+1)/2= ;var w2=3D1-w1;var rgb=3D[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w= 1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=3Dcolor1.al= pha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=3Dfun= ction(start_color,end_color,start_value,end_value){this.start_color=3Dnew C= olor(start_color);this.end_color=3Dnew Color(end_color);this.start_value=3D= start_value;this.end_value=3Dend_value;this.value_range=3Dend_value-start_v= alue};LinearRamp.prototype.map_value=3Dfunction(value){value=3DMath.max(val= ue,this.start_value);value=3DMath.min(value,this.end_value);value=3D(value-= this.start_value)/this.value_range;return this.start_color.mix(this.end_col= or,1-value).toCSS()};var SplitRamp=3Dfunction(start_color,middle_color,end_= color,start_value,end_value){this.positive_ramp=3Dnew LinearRamp(middle_col= or,end_color,0,end_value);this.negative_ramp=3Dnew LinearRamp(middle_color,= start_color,0,-start_value);this.start_value=3Dstart_value;this.end_value= =3Dend_value};SplitRamp.prototype.map_value=3Dfunction(value){value=3DMath.= max(value,this.start_value);value=3DMath.min(value,this.end_value);if(value= >=3D0){return this.positive_ramp.map_value(value)}else{return this.negative= _ramp.map_value(-value)}};var DiagonalHeatmapPainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][5])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][5])}this.= prefs.max_value=3Dmax_value}};DiagonalHeatmapPainter.prototype.default_pref= s=3D{min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8= C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=3Dfunction(= ctx,width,height,w_scale){var min_value=3Dthis.prefs.min_value,max_value=3D= this.prefs.max_value,value_range=3Dmax_value-min_value,height_px=3Dheight,v= iew_start=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data,invsqrt2=3D1/= Math.sqrt(2);var ramp=3D(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.= prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=3Df= unction(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/= 180);ctx.scale(invsqrt2,invsqrt2);for(var i=3D0,len=3Ddata.length;i<len;i++= ){d=3Ddata[i];s1=3Dscale(d[1]);e1=3Dscale(d[2]);s2=3Dscale(d[4]);e2=3Dscale= (d[5]);value=3Dd[6];ctx.fillStyle=3D(ramp.map_value(value));ctx.fillRect(s1= ,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter= :SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeat= urePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeature= Painter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/tr= ackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filter= s"],function(ab,x,l,u,L,Z,i){var q=3Dab.extend;var V=3Dfunction(ac){return(= "isResolved" in ac)};var n=3D{};var k=3Dfunction(ac,ad){n[ac.attr("id")]=3D= ad};var m=3Dfunction(ac,ae,ag,af){ag=3D".group";var ad=3D{};n[ac.attr("id")= ]=3Daf;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an= =3D$(this),at=3D$(this).parent(),ak=3Dat.children(),am=3Dn[$(this).attr("id= ")],aj,ai,aq,ah,al;ai=3D$(this).parents(ag);if(ai.length!=3D=3D0){aq=3Dai.p= osition().top;ah=3Daq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefo= re(ai);var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_dr= awable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);= var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(= am);return}}}ai=3Dnull;for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));aq= =3Daj.position().top;ah=3Daq+aj.outerHeight();if(aj.is(ag)&&this!=3D=3Daj.g= et(0)&&ap.offsetY>=3Daq&&ap.offsetY<=3Dah){if(ap.offsetY-aq<ah-ap.offsetY){= aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(t= his)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add= _drawable(am);return}}for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));if(a= p.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass(= "intro"))){break}}if(al=3D=3D=3Dak.length){if(this!=3D=3Dak.get(al-1)){at.a= ppend(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!=3D=3Dak.ge= t(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(= ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=3Dac= .css("border-top");ad["border-bottom"]=3Dac.css("border-bottom");$(this).cs= s({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind(= "dragend",function(){$(this).css(ad)})};exports.moveable=3Dm;var aa=3D16,G= =3D9,D=3D20,A=3D100,I=3D12000,S=3D400,K=3D5000,w=3D100,o=3D"There was an er= ror in indexing this dataset. ",J=3D"A converter for this dataset is not in= stalled. Please check your datatypes_conf.xml file.",E=3D"No data for this = chrom/contig.",v=3D"Preparing data. This can take a while for a large datas= et. If the visualization is saved and closed, preparation will continue in = the background.",y=3D"Tool cannot be rerun: ",a=3D"Loading data...",U=3D"Re= ady for display",Q=3D10,H=3D20;function W(ad,ac){if(!ac){ac=3D0}var ae=3DMa= th.pow(10,ac);return Math.round(ad*ae)/ae}var r=3Dfunction(ad,ac,af){if(!r.= id_counter){r.id_counter=3D0}this.id=3Dr.id_counter++;this.name=3Daf.name;t= his.view=3Dad;this.container=3Dac;this.config=3Dnew F({track:this,params:[{= key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:= af.prefs,onchange:function(){this.track.set_name(this.track.config.values.n= ame)}});this.prefs=3Dthis.config.values;this.drag_handle_class=3Daf.drag_ha= ndle_class;this.is_overview=3Dfalse;this.action_icons=3D{};this.content_vis= ible=3Dtrue;this.container_div=3Dthis.build_container_div();this.header_div= =3Dthis.build_header_div();if(this.header_div){this.container_div.append(th= is.header_div);this.icons_div=3D$("<div/>").css("float","left").hide().appe= ndTo(this.header_div);this.build_action_icons(this.action_icons_def);this.h= eader_div.append($("<div style=3D'clear: both'/>"));this.header_div.dblclic= k(function(ag){ag.stopPropagation()});var ae=3Dthis;this.container_div.hove= r(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div = style=3D'clear: both'/>").appendTo(this.container_div)}};r.prototype.action= _icons_def=3D[{name:"toggle_icon",title:"Hide/show content",css_class:"togg= le",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_= icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.= content_visible=3Dfalse}else{ac.action_icons.toggle_icon.addClass("toggle")= .removeClass("toggle-expand");ac.content_visible=3Dtrue;ac.show_contents()}= }},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on= _click_fn:function(ad){var af=3Dfunction(){hide_modal();$(window).unbind("k= eypress.check_enter_esc")},ac=3Dfunction(){ad.config.update_from_form($(".d= ialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae= =3Dfunction(ag){if((ag.keyCode||ag.which)=3D=3D=3D27){af()}else{if((ag.keyC= ode||ag.which)=3D=3D=3D13){ac()}}};$(window).bind("keypress.check_enter_esc= ",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{n= ame:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:functi= on(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:functio= n(){},changed:function(){this.view.changed()},can_draw:function(){if(this.e= nabled&&this.content_visible){return true}return false},request_draw:functi= on(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.o= ld_name=3Dthis.name;this.name=3Dac;this.name_div.text(this.name)},revert_na= me:function(){if(this.old_name){this.name=3Dthis.old_name;this.name_div.tex= t(this.name)}},remove:function(){this.changed();this.container.remove_drawa= ble(this);var ac=3Dthis.view;this.container_div.hide(0,function(){$(this).r= emove();ac.update_intro_div()})},build_container_div:function(){},build_hea= der_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=3Dt= his;this.action_icons[ad]=3D$("<a/>").attr("href","javascript:void(0);").at= tr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(functio= n(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}}= ,build_action_icons:function(ac){var ae;for(var ad=3D0;ad<ac.length;ad++){a= e=3Dac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_f= n,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){= },show_contents:function(){},get_drawables:function(){}});var z=3Dfunction(= ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=3Dae.obj_type;this.drawables= =3D[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawab= les=3D[];var ad;for(var ac=3D0;ac<ae.length;ac++){ad=3Dp(ae[ac],this.view,t= his);this.add_drawable(ad)}},init:function(){for(var ac=3D0;ac<this.drawabl= es.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=3D0= ;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:functi= on(){var ad=3D[];for(var ac=3D0;ac<this.drawables.length;ac++){ad.push(this= .drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:t= his.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(a= c);ac.container=3Dthis;this.changed()},add_drawable_before:function(ae,ac){= this.changed();var ad=3Dthis.drawables.indexOf(ac);if(ad!=3D=3D-1){this.dra= wables.splice(ad,0,ae);return true}return false},replace_drawable:function(= ae,ac,ad){var af=3Dthis.drawables.indexOf(ae);if(af!=3D=3D-1){this.drawable= s[af]=3Dac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.chang= ed()}return af},remove_drawable:function(ad){var ac=3Dthis.drawables.indexO= f(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);ad.container=3Dnull;this.= changed();return true}return false},move_drawable:function(ad,ae){var ac=3D= this.drawables.indexOf(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);this= .drawables.splice(ae,0,ad);this.changed();return true}return false},get_dra= wables:function(){return this.drawables}});var P=3Dfunction(ad,ac,af){q(af,= {obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad= ,ac,af);this.content_div=3D$("<div/>").addClass("content-div").attr("id","g= roup_"+this.id+"_content_div").appendTo(this.container_div);k(this.containe= r_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_= class,".group",this);this.filters_manager=3Dnew i.FiltersManager(this);this= .header_div.after(this.filters_manager.parent_div);this.saved_filters_manag= ers=3D[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filt= ers" in af){var ae=3Dthis.filters_manager;this.filters_manager=3Dnew i.Filt= ersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.= parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P= .prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_ic= ons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Sh= ow composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".b= s-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title= :"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_= manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_ma= nagers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filt= ers_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div= :function(){var ac=3D$("<div/>").addClass("group").attr("id","group_"+this.= id);if(this.container){this.container.content_div.append(ac)}return ac},bui= ld_header_div:function(){var ac=3D$("<div/>").addClass("track-header");ac.a= ppend($("<div/>").addClass(this.drag_handle_class));this.name_div=3D$("<div= />").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_co= ntents:function(){this.tiles_div.hide()},show_contents:function(){this.tile= s_div.show();this.request_draw()},update_icons:function(){var ae=3Dthis.dra= wables.length;if(ae=3D=3D=3D0){this.action_icons.composite_icon.hide();this= .action_icons.filters_icon.hide()}else{if(ae=3D=3D=3D1){if(this.drawables[0= ] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.f= ilters_icon.hide()}else{var al,ak,ai,ao=3Dtrue,ag=3Dthis.drawables[0].get_t= ype(),ac=3D0;for(al=3D0;al<ae;al++){ai=3Dthis.drawables[al];if(ai.get_type(= )!=3D=3Dag){can_composite=3Dfalse;break}if(ai instanceof c){ac++}}if(ao||ac= =3D=3D=3D1){this.action_icons.composite_icon.show()}else{this.action_icons.= composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac=3D=3D=3Dthis.dr= awables.length){var ap=3D{},ad;ai=3Dthis.drawables[0];for(ak=3D0;ak<ai.filt= ers_manager.filters.length;ak++){ad=3Dai.filters_manager.filters[ak];ap[ad.= name]=3D[ad]}for(al=3D1;al<this.drawables.length;al++){ai=3Dthis.drawables[= al];for(ak=3D0;ak<ai.filters_manager.filters.length;ak++){ad=3Dai.filters_m= anager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_ma= nager.remove_all();var af,ah,aj,am;for(var an in ap){af=3Dap[an];if(af.leng= th=3D=3D=3Dac){ah=3Dnew i.NumberFilter({name:af[0].name,index:af[0].index})= ;this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.lengt= h>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_i= con.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_= managers:function(){for(var ac=3D0;ac<this.drawables.length;ac++){this.draw= ables[ac].filters_manager=3Dthis.saved_filters_managers[ac]}this.saved_filt= ers_managers=3D[]},setup_multitrack_filtering:function(){if(this.filters_ma= nager.filters.length>0){this.saved_filters_managers=3D[];for(var ac=3D0;ac<= this.drawables.length;ac++){drawable=3Dthis.drawables[ac];this.saved_filter= s_managers.push(drawable.filters_manager);drawable.filters_manager=3Dthis.f= ilters_manager}}this.filters_manager.init_filters()},show_composite_track:f= unction(){var ag=3D[];for(var ad=3D0;ad<this.drawables.length;ad++){ag.push= (this.drawables[ad].name)}var ae=3D"Composite Track of "+this.drawables.len= gth+" tracks ("+ag.join(", ")+")";var af=3Dnew f(this.view,this.view,{name:= ae,drawables:this.drawables});var ac=3Dthis.container.replace_drawable(this= ,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_draw= able.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prot= otype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function()= {if(this.filters_manager.visible()){this._restore_filter_managers()}var ac= =3Dq(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()= });if(this.filters_manager.visible()){this.setup_multitrack_filtering()}ret= urn ac},request_draw:function(ac,ae){for(var ad=3D0;ad<this.drawables.lengt= h;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Y=3Dfunction(ac){q(a= c,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=3Dnull;= this.vis_id=3Dac.vis_id;this.dbkey=3Dac.dbkey;this.label_tracks=3D[];this.t= racks_to_be_redrawn=3D[];this.max_low=3D0;this.max_high=3D0;this.zoom_facto= r=3D3;this.min_separation=3D30;this.has_changes=3Dfalse;this.load_chroms_de= ferred=3Dnull;this.init();this.canvas_manager=3Dnew x.CanvasManager(this.co= ntainer.get(0).ownerDocument);this.reset()};ab.extend(Y.prototype,Backbone.= Events);q(Y.prototype,z.prototype,{init:function(){this.requested_redraw=3D= false;var ae=3Dthis.container,ac=3Dthis;this.top_container=3D$("<div/>").ad= dClass("top-container").appendTo(ae);this.browser_content_div=3D$("<div/>")= .addClass("content").css("position","relative").appendTo(ae);this.bottom_co= ntainer=3D$("<div/>").addClass("bottom-container").appendTo(ae);this.top_la= beltrack=3D$("<div/>").addClass("top-labeltrack").appendTo(this.top_contain= er);this.viewport_container=3D$("<div/>").addClass("viewport-container").at= tr("id","viewport-container").appendTo(this.browser_content_div);this.conte= nt_div=3Dthis.viewport_container;k(this.viewport_container,ac);this.intro_d= iv=3D$("<div/>").addClass("intro").appendTo(this.viewport_container).hide()= ;var af=3D$("<div/>").text("Add Datasets to Visualization").addClass("actio= n-button").appendTo(this.intro_div).click(function(){x.select_datasets(sele= ct_datasets_url,add_track_async_url,ac.dbkey,function(ag){ab.each(ag,functi= on(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=3D$("<div/>")= .addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_contai= ner=3D$("<div/>").addClass("trackster-nav-container").prependTo(this.top_co= ntainer);this.nav=3D$("<div/>").addClass("trackster-nav").appendTo(this.nav= _container);this.overview=3D$("<div/>").addClass("overview").appendTo(this.= bottom_container);this.overview_viewport=3D$("<div/>").addClass("overview-v= iewport").appendTo(this.overview);this.overview_close=3D$("<a/>").attr("hre= f","javascript:void(0);").attr("title","Close overview").addClass("icon-but= ton overview-close tooltip").hide().appendTo(this.overview_viewport);this.o= verview_highlight=3D$("<div/>").addClass("overview-highlight").hide().appen= dTo(this.overview_viewport);this.overview_box_background=3D$("<div/>").addC= lass("overview-boxback").appendTo(this.overview_viewport);this.overview_box= =3D$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);th= is.default_overview_height=3Dthis.overview_box.height();this.nav_controls= =3D$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_selec= t=3D$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option= value=3D''>Loading</option>").appendTo(this.nav_controls);var ad=3Dfunctio= n(ag){if(ag.type=3D=3D=3D"focusout"||(ag.keyCode||ag.which)=3D=3D=3D13||(ag= .keyCode||ag.which)=3D=3D=3D27){if((ag.keyCode||ag.which)!=3D=3D27){ac.go_t= o($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.= chrom_select.show()}};this.nav_input=3D$("<input/>").addClass("nav-input").= hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_= span=3D$("<span/>").addClass("location").attr("original-title","Click to ch= ange location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);t= his.location_span.click(function(){ac.location_span.hide();ac.chrom_select.= hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("= display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_= input.autocomplete({source:function(ai,ag){var aj=3D[],ah=3D$.map(ac.get_dr= awables(),function(ak){return ak.data_manager.search_features(ai.term).succ= ess(function(al){aj=3Daj.concat(al)})});$.when.apply($,ah).done(function(){= ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.= vis_id!=3D=3Dundefined){this.hidden_input=3D$("<input/>").attr("type","hidd= en").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=3D$("<a/>").= attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}= ).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_co= ntrols);this.zi_link=3D$("<a/>").attr("id","zoom-in").attr("title","Zoom in= ").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_r= edraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=3Dthis.load= _chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom= (ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(thi= s).find("input").trigger("blur")});this.browser_content_div.bind("dblclick"= ,function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_= box.bind("dragstart",function(ag,ah){this.current_x=3Dah.offsetX}).bind("dr= ag",function(ag,ai){var aj=3Dai.offsetX-this.current_x;this.current_x=3Dai.= offsetX;var ah=3DMath.round(aj/ac.viewport_container.width()*(ac.max_high-a= c.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.re= set_overview()});this.viewport_container.bind("draginit",function(ag,ah){if= (ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragsta= rt",function(ag,ah){ah.original_low=3Dac.low;ah.current_height=3Dag.clientY= ;ah.current_x=3Dah.offsetX}).bind("drag",function(ai,ak){var ag=3D$(this);v= ar al=3Dak.offsetX-ak.current_x;var ah=3Dag.scrollTop()-(ai.clientY-ak.curr= ent_height);ag.scrollTop(ah);ak.current_height=3Dai.clientY;ak.current_x=3D= ak.offsetX;var aj=3DMath.round(al/ac.viewport_container.width()*(ac.high-ac= .low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){a= h*=3D50;var aj=3DMath.round(-ah/ac.viewport_container.width()*(ac.high-ac.l= ow));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,= ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_= labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolu= te","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this)= )}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.= startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var= ah=3DMath.min(ak.pageX,al.startX)-ac.container.offset().left,ag=3DMath.max= (ak.pageX,al.startX)-ac.container.offset().left,aj=3D(ac.high-ac.low),ai=3D= ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.lo= w,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=3DMa= th.min(al.pageX,am.startX),ag=3DMath.max(al.pageX,am.startX),aj=3D(ac.high-= ac.low),ai=3Dac.viewport_container.width(),ak=3Dac.low;ac.low=3DMath.round(= ah/ai*aj)+ak;ac.high=3DMath.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.requ= est_redraw()});this.add_label_track(new X(this,{content_div:this.top_labelt= rack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}))= ;$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this= .resize_timer)}this.resize_timer=3DsetTimeout(function(){ac.resize_window()= },500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(= window).trigger("resize")},changed:function(){this.has_changes=3Dtrue},upda= te_intro_div:function(){if(this.drawables.length=3D=3D=3D0){this.intro_div.= show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){= if(this.timer){clearTimeout(this.timer)}if(ag){var ae=3Dthis;this.timer=3Ds= etTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{vie= w.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){th= is.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val= (this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=3Dview.chrom_select= .val();if(ad!=3D=3D""){this.trigger_navigate(ad,view.low,view.high,true)}},= load_chroms:function(ae){ae.num=3Dw;var ac=3Dthis,ad=3D$.Deferred();$.ajax(= {url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){= if(ag.chrom_info.length=3D=3D=3D0){return}if(ag.reference){ac.add_label_tra= ck(new B(ac))}ac.chrom_data=3Dag.chrom_info;var aj=3D'<option value=3D"">Se= lect Chrom/Contig</option>';for(var ai=3D0,af=3Dac.chrom_data.length;ai<af;= ai++){var ah=3Dac.chrom_data[ai].chrom;aj+=3D'<option value=3D"'+ah+'">'+ah= +"</option>"}if(ag.prev_chroms){aj+=3D'<option value=3D"previous">Previous = '+w+"</option>"}if(ag.next_chroms){aj+=3D'<option value=3D"next">Next '+w+"= </option>"}ac.chrom_select.html(aj);ac.chrom_start_index=3Dag.start_index;a= d.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey= :",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=3Dthis;if= (!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah= ,ad,aj)});return}if(!ah||ah=3D=3D=3D"None"){return}if(ah=3D=3D=3D"previous"= ){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah=3D=3D=3D"next= "){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=3D$.grep(ae= .chrom_data,function(ak,al){return ak.chrom=3D=3D=3Dah})[0];if(ai=3D=3D=3Du= ndefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});= return}else{if(ah!=3D=3Dae.chrom){ae.chrom=3Dah;ae.chrom_select.val(ae.chro= m);ae.max_high=3Dai.len-1;ae.reset();ae.request_redraw(true);for(var ag=3D0= ,ac=3Dae.drawables.length;ag<ac;ag++){var af=3Dae.drawables[ag];if(af.init)= {af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!=3D=3Du= ndefined&&aj!=3D=3Dundefined){ae.low=3DMath.max(ad,0);ae.high=3DMath.min(aj= ,ae.max_high)}else{ae.low=3D0;ae.high=3Dae.max_high}ae.reset_overview();ae.= request_redraw()}},go_to:function(ag){ag=3Dag.replace(/ |,/g,"");var ak=3Dt= his,ac,af,ad=3Dag.split(":"),ai=3Dad[0],aj=3Dad[1];if(aj!=3D=3Dundefined){t= ry{var ah=3Daj.split("-");ac=3DparseInt(ah[0],10);af=3DparseInt(ah[1],10)}c= atch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae= ){var ac=3Dthis;var ad=3Dac.high-ac.low;this.move_delta(ae*ad)},move_delta:= function(af){var ac=3Dthis;var ae=3Dac.high-ac.low;if(ac.low-af<ac.max_low)= {ac.low=3Dac.max_low;ac.high=3Dac.max_low+ae}else{if(ac.high-af>ac.max_high= ){ac.high=3Dac.max_high;ac.low=3Dac.max_high-ae}else{ac.high-=3Daf;ac.low-= =3Daf}}ac.request_redraw();var ad=3Dac.chrom_select.val();this.trigger_navi= gate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_dra= wable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_l= abel_track:function(ac){ac.view=3Dthis;ac.init();this.label_tracks.push(ac)= },remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae)= ;if(ad){var ac=3Dthis;ae.container_div.hide(0,function(){$(this).remove();a= c.update_intro_div()})}},reset:function(){this.low=3Dthis.max_low;this.high= =3Dthis.max_high;this.viewport_container.find(".yaxislabel").remove()},requ= est_redraw:function(ak,ac,aj,al){var ai=3Dthis,ah=3D(al?[al]:ai.drawables),= ae;var ad;for(var ag=3D0;ag<ah.length;ag++){ad=3Dah[ag];ae=3D-1;for(var af= =3D0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af]= [0]=3D=3D=3Dad){ae=3Daf;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac= ,aj])}else{ai.tracks_to_be_redrawn[ag][1]=3Dac;ai.tracks_to_be_redrawn[ag][= 2]=3Daj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._re= draw(ak)});this.requested_redraw=3Dtrue}},_redraw:function(am){this.request= ed_redraw=3Dfalse;var aj=3Dthis.low,af=3Dthis.high;if(aj<this.max_low){aj= =3Dthis.max_low}if(af>this.max_high){af=3Dthis.max_high}var al=3Dthis.high-= this.low;if(this.high!=3D=3D0&&al<this.min_separation){af=3Daj+this.min_sep= aration}this.low=3DMath.floor(aj);this.high=3DMath.ceil(af);this.update_loc= ation(this.low,this.high);this.resolution_b_px=3D(this.high-this.low)/this.= viewport_container.width();this.resolution_px_b=3Dthis.viewport_container.w= idth()/(this.high-this.low);var ac=3D(this.low/(this.max_high-this.max_low)= *this.overview_viewport.width())||0;var ai=3D((this.high-this.low)/(this.ma= x_high-this.max_low)*this.overview_viewport.width())||0;var an=3D13;this.ov= erview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overv= iew_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_= highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=3D0,ah=3D= this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=3Dthis.tracks_to_be_redrawn= [ag][0];ad=3Dthis.tracks_to_be_redrawn[ag][1];ak=3Dthis.tracks_to_be_redraw= n[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=3D[];for(ag=3D0,= ah=3Dthis.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},= zoom_in:function(ad,ae){if(this.max_high=3D=3D=3D0||this.high-this.low<=3Dt= his.min_separation){return}var af=3Dthis.high-this.low,ag=3Daf/2+this.low,a= c=3D(af/this.zoom_factor)/2;if(ad){ag=3Dad/this.viewport_container.width()*= (this.high-this.low)+this.low}this.low=3DMath.round(ag-ac);this.high=3DMath= .round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(= this.max_high=3D=3D=3D0){return}var ad=3Dthis.high-this.low,ae=3Dad/2+this.= low,ac=3D(ad*this.zoom_factor)/2;this.low=3DMath.round(ae-ac);this.high=3DM= ath.round(ae+ac);this.changed();this.request_redraw()},resize_window:functi= on(){this.viewport_container.height(this.container.height()-this.top_contai= ner.height()-this.bottom_container.height());this.request_redraw()},set_ove= rview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dat= aset_id=3D=3D=3Dae.dataset_id){return}this.overview_viewport.find(".track")= .remove()}var ad=3Dae.copy({content_div:this.overview_viewport}),ac=3Dthis;= ad.header_div.hide();ad.is_overview=3Dtrue;ac.overview_drawable=3Dad;this.o= verview_drawable.postdraw_actions=3Dfunction(){ac.overview_highlight.show()= .height(ac.overview_drawable.content_div.height());ac.overview_viewport.hei= ght(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight()= );ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request= _draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove()= ;this.overview_viewport.find(".track-tile").remove();this.overview_viewport= .height(this.default_overview_height);this.overview_box.height(this.default= _overview_height);this.overview_close.hide();this.overview_highlight.hide()= ;view.resize_window();view.overview_drawable=3Dnull}});var s=3Dfunction(ae,= aj,af){this.track=3Dae;this.name=3Daj.name;this.params=3D[];var aq=3Daj.par= ams;for(var ag=3D0;ag<aq.length;ag++){var al=3Daq[ag],ad=3Dal.name,ap=3Dal.= label,ah=3Dunescape(al.html),ar=3Dal.value,an=3Dal.type;if(an=3D=3D=3D"numb= er"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}e= lse{if(an=3D=3D=3D"select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad= ]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an= )}}}this.parent_div=3D$("<div/>").addClass("dynamic-tool").hide();this.pare= nt_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){a= u.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});v= ar ao=3D$("<div class=3D'tool-name'>").appendTo(this.parent_div).text(this.= name);var am=3Dthis.params;var ak=3Dthis;$.each(this.params,function(av,ay)= {var ax=3D$("<div>").addClass("param-row").appendTo(ak.parent_div);var au= =3D$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=3D= $("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":in= put").val(ay.value);$("<div style=3D'clear: both;'/>").appendTo(ax)});this.= parent_div.find("input").click(function(){$(this).select()});var at=3D$("<d= iv>").addClass("param-row").appendTo(this.parent_div);var ai=3D$("<input ty= pe=3D'submit'>").attr("value","Run on complete dataset").appendTo(at);var a= c=3D$("<input type=3D'submit'>").attr("value","Run on visible region").css(= "margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});= ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){t= his.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac= =3D0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dic= t:function(){var ad=3D{};for(var ac=3D0;ac<this.params.length;ac++){ad[this= .params[ac].name]=3Dthis.params[ac].value}ad.visible=3Dthis.parent_div.is("= :visible");return ad},get_param_values_dict:function(){var ac=3D{};this.par= ent_div.find(":input").each(function(){var ad=3D$(this).attr("name"),ae=3D$= (this).val();ac[ad]=3Dae});return ac},get_param_values:function(){var ac=3D= [];this.parent_div.find(":input").each(function(){var ad=3D$(this).attr("na= me"),ae=3D$(this).val();if(ad){ac[ac.length]=3Dae}});return ac},run_on_data= set:function(){var ac=3Dthis;ac.run({target_dataset_id:this.track.original_= dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Runni= ng",ac.name+" is running on the complete dataset. 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Z.Dataset(aj));ai.tiles_div.text("Running job."= );ai.init()})},run:function(ac,ae,af){ac.inputs=3Dthis.get_param_values_dic= t();var ad=3Dnew l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get= ("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"applicati= on/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=3D= =3D"pending"}});$.when(ad.go()).then(function(ag){if(ag=3D=3D=3D"no convert= er"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.e= rror){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}= else{af(ag)}}})}});var N=3Dfunction(ad,ac,ae,af){this.name=3Dad;this.label= =3Dac;this.html=3D$(ae);this.value=3Daf};q(N.prototype,{update_value:functi= on(){this.value=3D$(this.html).val()}});var e=3Dfunction(ae,ad,ag,ah,af,ac)= {N.call(this,ae,ad,ag,ah);this.min=3Daf;this.max=3Dac};q(e.prototype,N.prot= otype,{update_value:function(){N.prototype.update_value.call(this);this.val= 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m({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new= Backbone.Collection(al).toJSON())})},ag=3Dfunction(ai){if((ai.keyCode||ai.= which)=3D=3D=3D27){ah()}else{if((ai.keyCode||ai.which)=3D=3D=3D13){ad()}}};= show_modal("Visualize tool parameter space and output from different parame= ter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_dr= aw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return t= rue}return false},build_container_div:function(){return $("<div/>").addClas= s("track").attr("id","track_"+this.id).css("position","relative")},build_he= ader_div:function(){var ac=3D$("<div class=3D'track-header'/>");if(this.vie= w.editor){this.drag_div=3D$("<div/>").addClass(this.drag_handle_class).appe= ndTo(ac)}this.name_div=3D$("<div/>").addClass("track-name").appendTo(ac).te= xt(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\= -]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle= 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ac=3Dthis;if(ac.filters_availabl= e){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hi= de()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_sp= ace_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.= param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return= ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(fa= lse,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.ca= n_draw()){return}var al=3Dthis.view.low,ah=3Dthis.view.high,aj=3Dah-al,ae= =3Dthis.view.container.width(),ap=3Dthis.view.resolution_px_b,ag=3Dthis.vie= w.resolution_b_px;if(this.is_overview){al=3Dthis.view.max_low;ah=3Dthis.vie= w.max_high;ag=3D(view.max_high-view.max_low)/ae;ap=3D1/ag}this.before_draw(= );this.tiles_div.children().addClass("remove");var ac=3DMath.floor(al/(ag*S= )),ak=3Dtrue,ao=3D[],ai=3Dfunction(aq){return(aq&&"track" in aq)};while((ac= *S*ag)<ah){var am=3Dthis.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(a= m)){ao.push(am)}else{ak=3Dfalse}ac+=3D1}if(!an){this.tiles_div.children(".r= emove").removeClass("remove").remove()}var af=3Dthis;if(ak){this.tiles_div.= children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_ac= tions:function(ae,af,ah,ac){var ag=3Dfalse;for(var ad=3D0;ad<ae.length;ad++= ){if(ae[ad].has_icons){ag=3Dtrue;break}}if(ag){for(var ad=3D0;ad<ae.length;= ad++){tile=3Dae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}= }}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=3Dthis,ax=3Dthis._gen= _tile_cache_key(ao,ai,au),af=3Dthis._get_tile_bounds(au,ar);if(!ap){ap=3D{}= }var aw=3D(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,a= h,ai);return aw}var al=3Dtrue;var at=3Dan.data_manager.get_data(af,an.mode,= ar,an.data_url_extra_params);if(V(at)){al=3Dfalse}var aj;if(view.reference_= track&&ai>view.canvas_manager.char_width_px){aj=3Dview.reference_track.data= _manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params)= ;if(V(aj)){al=3Dfalse}}if(al){q(at,ap.more_tile_data);var ak=3Dan.mode;if(a= k=3D=3D=3D"Auto"){ak=3Dan.get_mode(at);an.update_auto_mode(ak)}var ae=3Dan.= view.canvas_manager.new_canvas(),av=3Daf.get("start"),ad=3Daf.get("end"),ao= =3DMath.ceil((ad-av)*ai)+an.left_offset,am=3Dan.get_canvas_height(at,ak,ai,= ao);ae.width=3Dao;ae.height=3Dam;var aq=3Dae.getContext("2d");aq.translate(= this.left_offset,0);var aw=3Dan.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!=3D= =3Dundefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw= }var ag=3D$.Deferred();$.when(at,aj).then(function(){view.request_redraw(fa= lse,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac= ,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag= ,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},sh= ow_tile:function(ae,ah,ai){var ad=3Dthis,ac=3Dae.html_elt;ae.predisplay_act= ions();var ag=3D(ae.low-(this.is_overview?this.view.max_low:this.view.low))= *ai;if(this.left_offset){ag-=3Dthis.left_offset}ac.css({position:"absolute"= ,top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah= .append(ac)}ae.html_elt.height("auto");this.max_height_px=3DMath.max(this.m= ax_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("hei= ght",this.max_height_px+"px");var af=3Dthis.max_height_px;if(this.visible_h= eight_px!=3D=3D0){af=3DMath.min(this.max_height_px,this.visible_height_px)}= this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var = af=3DMath.floor(ac*S*ad),ag=3DMath.ceil(S*ad),ae=3D(af+ag<=3Dthis.view.max_= high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.c= hrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){v= ar ad=3Dthis,ag=3D(ae!=3D=3Dundefined&&ac!=3D=3Dundefined&&af!=3D=3Dundefin= ed?ae+":"+ac+"-"+af:"all");return" - region=3D["+ag+"], parameters=3D["+ad.= tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(a= c,ad){return true},can_subset:function(ac){return false},init_for_tool_data= :function(){this.data_manager.set("data_type","raw_data");this.data_query_w= ait=3D1000;this.dataset_check_type=3D"state";this.normal_postdraw_actions= =3Dthis.postdraw_actions;this.postdraw_actions=3Dfunction(ae,af,ah,ac){var = ad=3Dthis;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type=3D"= converted_datasets_state";ad.data_query_wait=3DK;var ag=3Dnew l.ServerState= Deferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda= _ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){retu= rn ai!=3D=3D"pending"}});$.when(ag.go()).then(function(){ad.data_manager.se= t("data_type","data")});ad.postdraw_actions=3Dad.normal_postdraw_actions}}}= );var X=3Dfunction(ad,ac){var ae=3D{resize:false};g.call(this,ad,ac,ae);thi= s.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_h= eader_div:function(){},init:function(){this.enabled=3Dtrue},_draw:function(= ){var ae=3Dthis.view,af=3Dae.high-ae.low,ai=3DMath.floor(Math.pow(10,Math.f= loor(Math.log(af)/Math.log(10)))),ac=3DMath.floor(ae.low/ai)*ai,ag=3Dthis.v= iew.container.width(),ad=3D$("<div style=3D'position: relative; height: 1.3= em;'></div>");while(ac<ae.high){var ah=3D(ac-ae.low)/af*ag;ad.append($("<di= v class=3D'label'>"+commatize(ac)+"</div>").css({position:"absolute",left:a= h-1}));ac+=3Dai}this.content_div.children(":first").remove();this.content_d= iv.append(ad)}});var f=3Dfunction(ad,ac,ag){M.call(this,ad,ac,ag);this.draw= ables=3D[];this.left_offset=3D0;if("drawables" in ag){var af;for(var ae=3D0= ;ae<ag.drawables.length;ae++){af=3Dag.drawables[ae];this.drawables[ae]=3Dp(= af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=3Daf.left_= offset}}this.enabled=3Dtrue}if(this.drawables.length!=3D=3D0){this.set_disp= lay_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.upda= te_icons();this.obj_type=3D"CompositeTrack"};q(f.prototype,M.prototype,{act= ion_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_cl= ass:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.sh= ow_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_d= ict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpa= ck_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac)= ;for(var ad=3D0;ad<this.drawables.length;ad++){this.drawables[ad].change_mo= de(ac)}},init:function(){var ae=3D[];for(var ad=3D0;ad<this.drawables.lengt= h;ad++){ae.push(this.drawables[ad].init())}var ac=3Dthis;$.when.apply($,ae)= .then(function(){ac.enabled=3Dtrue;ac.request_draw()})},update_icons:functi= on(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hid= e();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can= _draw,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=3Dthis,aD=3Dthis._g= en_tile_cache_key(at,am,az),ah=3Dthis._get_tile_bounds(az,aw);if(!au){au=3D= {}}var aC=3D(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC= ,ak,am);return aC}var al=3D[],ar,ap=3Dtrue,ax,an;for(var ay=3D0;ay<this.dra= wables.length;ay++){ar=3Dthis.drawables[ay];ax=3Dar.data_manager.get_data(a= h,ar.mode,aw,ar.data_url_extra_params);if(V(ax)){ap=3Dfalse}al.push(ax);an= =3Dnull;if(view.reference_track&&am>view.canvas_manager.char_width_px){an= =3Dview.reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_= track.data_url_extra_params);if(V(an)){ap=3Dfalse}}al.push(an)}if(ap){q(ax,= au.more_tile_data);this.tile_predraw_init();var ag=3Dar.view.canvas_manager= .new_canvas(),ai=3Dar._get_tile_bounds(az,aw),aA=3Dah.get("start"),ae=3Dah.= get("end"),aB=3D0,at=3DMath.ceil((ae-aA)*am)+this.left_offset,aq=3D0,af=3D[= ],ay;var ac=3D0;for(ay=3D0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis= .drawables[ay];ax=3Dal[aB];var ao=3Dar.mode;if(ao=3D=3D=3D"Auto"){ao=3Dar.g= et_mode(ax);ar.update_auto_mode(ao)}af.push(ao);ac=3Dar.get_canvas_height(a= x,ao,am,at);if(ac>aq){aq=3Dac}}ag.width=3Dat;ag.height=3D(au.height?au.heig= ht:aq);aB=3D0;var av=3Dag.getContext("2d");av.translate(this.left_offset,0)= ;av.globalAlpha=3D0.5;av.globalCompositeOperation=3D"source-over";for(ay=3D= 0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawables[ay];ax=3Dal[aB= ];an=3Dal[aB+1];aC=3Dar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache= .set_elt(aD,aC);this.show_tile(aC,ak,am);return aC}var aj=3D$.Deferred(),ar= =3Dthis;$.when.apply($,al).then(function(){view.request_redraw(false,false,= false,ar);aj.resolve()});return aj},show_group:function(){var af=3Dnew P(th= is.view,this.container,{name:this.name}),ac;for(var ae=3D0;ae<this.drawable= s.length;ae++){ac=3Dthis.drawables[ae];ac.update_icons();af.add_drawable(ac= );ac.container=3Daf;af.content_div.append(ac.container_div)}var ad=3Dthis.c= ontainer.replace_drawable(this,af,true);af.request_draw()},tile_predraw_ini= t:function(){var af=3DNumber.MAX_VALUE,ac=3D-af,ad;for(var ae=3D0;ae<this.d= rawables.length;ae++){ad=3Dthis.drawables[ae];if(ad instanceof h){if(ad.pre= fs.min_value<af){af=3Dad.prefs.min_value}if(ad.prefs.max_value>ac){ac=3Dad.= prefs.max_value}}}for(var ae=3D0;ae<this.drawables.length;ae++){ad=3Dthis.d= rawables[ae];ad.prefs.min_value=3Daf;ad.prefs.max_value=3Dac}},postdraw_act= ions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,= ad);var ag=3D-1;for(var af=3D0;af<ae.length;af++){var ac=3Dae[af].html_elt.= find("canvas").height();if(ac>ag){ag=3Dac}}for(var af=3D0;af<ae.length;af++= ){var ai=3Dae[af];if(ai.html_elt.find("canvas").height()!=3D=3Dag){this.dra= w_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag}= );ai.html_elt.remove()}}}});var B=3Dfunction(ac){M.call(this,ac,{content_di= v:ac.top_labeltrack},{resize:false});ac.reference_track=3Dthis;this.left_of= fset=3D200;this.visible_height_px=3D12;this.container_div.addClass("referen= ce-track");this.content_div.css("background","none");this.content_div.css("= min-height","0px");this.content_div.css("border","none");this.data_url=3Dre= ference_url+"/"+this.view.dbkey;this.data_url_extra_params=3D{reference:tru= e};this.data_manager=3Dnew x.ReferenceTrackDataManager({data_url:this.data_= url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_he= ader_div:function(){},init:function(){this.data_manager.clear();this.enable= d=3Dtrue},can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah= ,ai,af){if(ai>this.view.canvas_manager.char_width_px){return M.prototype.dr= aw_helper.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return = null}},draw_tile:function(ak,al,ag,af,ai,am){var ae=3Dthis;if(am>this.view.= canvas_manager.char_width_px){if(ak.data=3D=3D=3Dnull){this.hide_contents()= ;return}var ad=3Dal.canvas;al.font=3Dal.canvas.manager.default_font;al.text= Align=3D"center";ak=3Dak.data;for(var ah=3D0,aj=3Dak.length;ah<aj;ah++){var= ac=3DMath.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();retu= rn new b(ae,ai,af,ad,ak)}this.hide_contents()}});var h=3Dfunction(ae,ad,af)= {var ac=3Dthis;this.display_modes=3D["Histogram","Line","Filled","Intensity= "];this.mode=3D"Histogram";M.call(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldd= a;this.dataset_id=3Daf.dataset_id;this.original_dataset_id=3Dthis.dataset_i= d;this.left_offset=3D0;this.config=3Dnew F({track:this,params:[{key:"name",= label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color= ",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"= Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Ma= x Value",type:"float",default_value:undefined},{key:"mode",type:"string",de= fault_value:this.mode,hidden:true},{key:"height",type:"int",default_value:3= 2,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.pr= efs.name);ac.vertical_range=3Dac.prefs.max_value-ac.prefs.min_value;ac.set_= min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.= prefs=3Dthis.config.values;this.visible_height_px=3Dthis.config.values.heig= ht;this.vertical_range=3Dthis.config.values.max_value-this.config.values.mi= n_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.r= equest_draw(true)},set_min_value:function(ac){this.prefs.min_value=3Dac;$("= #linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.til= e_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.= max_value=3Dac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.m= ax_value);this.tile_cache.clear();this.request_draw()},predraw_init:functio= n(){var ac=3Dthis;ac.vertical_range=3Dundefined;return $.getJSON(ac.dataset= .url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.= max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line= -track");var ag=3Dad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(p= arseFloat(ac.prefs.max_value))){var ae=3Dag.min,ai=3Dag.max;ae=3DMath.floor= (Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=3DMath.ceil(Math.max(0,Math.m= in(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=3Dae;ac.prefs.max_value=3Dai;$(= "#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.d= ataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=3Dac.prefs.m= ax_value-ac.prefs.min_value;ac.total_frequency=3Dag.total_frequency;ac.cont= ainer_div.find(".yaxislabel").remove();var ah=3D$("<div/>").text(W(ac.prefs= .min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs= -tooltip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)){ac.set_min_value= (aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id",= "linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=3D$("<= div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_fin= ish:function(aj){$(".bs-tooltip").remove();var aj=3DparseFloat(aj);if(!isNa= N(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxisla= bel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.cont= ainer_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=3Daj.canvas,af= =3Dag.get("start"),ai=3Dag.get("end"),ah=3Dnew L.LinePainter(al.data,af,ai,= this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac= ,al.data)},can_subset:function(ac){return false}});var t=3Dfunction(ae,ad,a= f){var ac=3Dthis;this.display_modes=3D["Heatmap"];this.mode=3D"Heatmap";M.c= all(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.dataset_id=3Daf.dataset= _id;this.original_dataset_id=3Dthis.dataset_id;this.left_offset=3D0;this.co= nfig=3Dnew F({track:this,params:[{key:"name",label:"Name",type:"text",defau= lt_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",de= fault_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color"= ,default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",d= efault_value:0},{key:"max_value",label:"Max Value",type:"float",default_val= ue:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"= height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,on= change:function(){ac.set_name(ac.prefs.name);ac.vertical_range=3Dac.prefs.m= ax_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max= _value(ac.prefs.max_value)}});this.prefs=3Dthis.config.values;this.visible_= height_px=3Dthis.config.values.height;this.vertical_range=3Dthis.config.val= ues.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.pro= totype,{on_resize:function(){this.request_draw(true)},set_min_value:functio= n(ac){this.prefs.min_value=3Dac;this.tile_cache.clear();this.request_draw()= },set_max_value:function(ac){this.prefs.max_value=3Dac;this.tile_cache.clea= r();this.request_draw()},draw_tile:function(am,ak,ah,af,ad,al){var ae=3Dak.= canvas,ac=3Dthis._get_tile_bounds(ad,af),ag=3Dac[0],aj=3Dac[1],ai=3Dnew L.D= iagonalHeatmapPainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.h= eight,al);return new b(this,ad,af,ae,am.data)}});var c=3Dfunction(af,ae,ah)= {var ad=3Dthis;this.display_modes=3D["Auto","Coverage","Dense","Squish","Pa= ck"];M.call(this,af,ae,ah);var ag=3Dl.get_random_color(),ac=3Dl.get_random_= color([ag,"#ffffff"]);this.config=3Dnew F({track:this,params:[{key:"name",l= abel:"Name",type:"text",default_value:this.name},{key:"block_color",label:"= Block color",type:"color",default_value:ag},{key:"reverse_strand_color",lab= el:"Antisense strand color",type:"color",default_value:ac},{key:"label_colo= r",label:"Label color",type:"color",default_value:"black"},{key:"show_count= s",label:"Show summary counts",type:"bool",default_value:true,help:"Show th= e number of items in each bin when drawing summary histogram"},{key:"histog= ram_max",label:"Histogram maximum",type:"float",default_value:null,help:"cl= ear value to set automatically"},{key:"connector_style",label:"Connector st= yle",type:"select",default_value:"fishbones",options:[{label:"Line with arr= ows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"stri= ng",default_value:this.mode,hidden:true},{key:"height",type:"int",default_v= alue:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:fu= nction(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_fr= om_config();ad.request_draw()}});this.prefs=3Dthis.config.values;this.visib= le_height_px=3Dthis.config.values.height;this.container_div.addClass("featu= re-track");this.hda_ldda=3Dah.hda_ldda;this.dataset_id=3Dah.dataset_id;this= .original_dataset_id=3Dah.dataset_id;this.show_labels_scale=3D0.001;this.sh= owing_details=3Dfalse;this.summary_draw_height=3D30;this.slotters=3D{};this= .start_end_dct=3D{};this.left_offset=3D200;this.set_painter_from_config()};= q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.datase= t_id=3Dac.get("id");this.hda_ldda=3Dac.get("hda_ldda");this.dataset=3Dac;th= is.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(th= is.config.values.connector_style=3D=3D=3D"arcs"){this.painter=3DL.ArcLinked= FeaturePainter}else{this.painter=3DL.LinkedFeaturePainter}},before_draw:fun= ction(){this.max_height_px=3D0},postdraw_actions:function(ar,am,ah,ag){M.pr= ototype.postdraw_actions.call(this,ar,ag);var al=3Dthis,ao;if(al.mode=3D=3D= =3D"Coverage"){var ad=3D-1;for(ao=3D0;ao<ar.length;ao++){var an=3Dar[ao].ma= x_val;if(an>ad){ad=3Dan}}for(ao=3D0;ao<ar.length;ao++){var au=3Dar[ao];if(a= u.max_val!=3D=3Dad){au.html_elt.remove();al.draw_helper(true,am,au.index,au= .resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filt= ers_manager){var ai=3Dal.filters_manager.filters;for(var aq=3D0;aq<ai.lengt= h;aq++){ai[aq].update_ui_elt()}var at=3Dfalse,ac,aj;for(ao=3D0;ao<ar.length= ;ao++){if(ar[ao].data.length){ac=3Dar[ao].data[0];for(var aq=3D0;aq<ai.leng= th;aq++){aj=3Dai[aq];if(aj.applies_to(ac)&&aj.min!=3D=3Daj.max){at=3Dtrue;b= reak}}}}if(al.filters_available!=3D=3Dat){al.filters_available=3Dat;if(!al.= filters_available){al.filters_manager.hide()}al.update_icons()}}this.contai= ner_div.find(".yaxislabel").remove();var af=3Dar[0];if(af instanceof j){var= ak=3D(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=3D$= ("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){= $(".bs-tooltip").remove();var av=3DparseFloat(av);al.prefs.histogram_max=3D= (!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Se= t max value; leave blank to use default"}).addClass("yaxislabel top").css("= color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanc= eof O){var ap=3Dtrue;for(ao=3D0;ao<ar.length;ao++){if(!ar[ao].all_slotted){= ap=3Dfalse;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else= {this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_= more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode= =3D=3D=3D"Auto"){if(ac=3D=3D=3D"no_detail"){ac=3D"feature spans"}else{if(ac= =3D=3D=3D"summary_tree"){ac=3D"coverage histogram"}}this.action_icons.mode_= icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slot= s:function(ag,ac,af){var ad=3Dthis.view.canvas_manager.dummy_context,ae=3Dt= his.slotters[ag];if(!ae||(ae.mode!=3D=3Daf)){ae=3Dnew (u.FeatureSlotter)(ag= ,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=3Dae}retur= n ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type=3D=3D=3D"s= ummary_tree"){mode=3D"summary_tree"}else{if(ac.extra_info=3D=3D=3D"no_detai= l"||this.is_overview){mode=3D"no_detail"}else{if(this.view.high-this.view.l= ow>I){mode=3D"Squish"}else{mode=3D"Pack"}}}return mode},get_canvas_height:f= unction(ac,ag,ah,ad){if(ag=3D=3D=3D"summary_tree"||ag=3D=3D=3D"Coverage"){r= eturn this.summary_draw_height}else{var af=3Dthis.incremental_slots(ah,ac.d= ata,ag);var ae=3Dnew (this.painter)(null,null,null,this.prefs,ag);return Ma= th.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,a= f,aj,ae){var ap=3Dthis,ad=3Daq.canvas,ay=3Daf.get("start"),ac=3Daf.get("end= "),ag=3Dthis.left_offset;if(ao=3D=3D=3D"summary_tree"||ao=3D=3D=3D"Coverage= "){var aA=3Dnew L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.wid= th,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=3D[],an=3D= this.slotters[aj].slots;all_slotted=3Dtrue;if(am.data){var ak=3Dthis.filter= s_manager.filters;for(var at=3D0,av=3Dam.data.length;at<av;at++){var ah=3Da= m.data[at];var au=3Dfalse;var al;for(var ax=3D0,aC=3Dak.length;ax<aC;ax++){= al=3Dak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=3Dtrue;break}}if(!au){a= i.push(ah);if(!(ah[0] in an)){all_slotted=3Dfalse}}}}var aB=3D(this.filters= _manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az= =3D(this.filters_manager.height_filter?new C(this.filters_manager.height_fi= lter):null);var aA=3Dnew (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);va= r aw=3Dnull;aq.fillStyle=3Dthis.prefs.block_color;aq.font=3Daq.canvas.manag= er.default_font;aq.textAlign=3D"right";if(am.data){aw=3DaA.draw(aq,ad.width= ,ad.height,aj,an);aw.translation=3D-ag}return new O(ap,af,ar,ad,am.data,aj,= ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(= ad=3D=3D=3D"Auto"){return true}else{if(ad=3D=3D=3D"Coverage"){return ac.dat= aset_type=3D=3D=3D"summary_tree"}else{if(ac.extra_info=3D=3D=3D"no_detail"|= |ac.dataset_type=3D=3D=3D"summary_tree"){return false}else{return true}}}},= can_subset:function(ac){if(ac.dataset_type=3D=3D=3D"summary_tree"||ac.messa= ge||ac.extra_info=3D=3D=3D"no_detail"){return false}return true}});var R=3D= function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=3Dnew F({track:this,pa= rams:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"b= lock_color",label:"Block color",type:"color",default_value:l.get_random_col= or()},{key:"label_color",label:"Label color",type:"color",default_value:"bl= ack"},{key:"show_insertions",label:"Show insertions",type:"bool",default_va= lue:false},{key:"show_counts",label:"Show summary counts",type:"bool",defau= lt_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:tru= e}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.trac= k.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});th= is.prefs=3Dthis.config.values;this.painter=3DL.ReadPainter};q(R.prototype,r= .prototype,M.prototype,c.prototype);var T=3Dfunction(ae,ad,ag){c.call(this,= ae,ad,ag);var af=3Dl.get_random_color(),ac=3Dl.get_random_color([af,"#fffff= f"]);this.config=3Dnew F({track:this,params:[{key:"name",label:"Name",type:= "text",default_value:this.name},{key:"block_color",label:"Block and sense s= trand color",type:"color",default_value:af},{key:"reverse_strand_color",lab= el:"Antisense strand color",type:"color",default_value:ac},{key:"label_colo= r",label:"Label color",type:"color",default_value:"black"},{key:"show_inser= tions",label:"Show insertions",type:"bool",default_value:false},{key:"show_= differences",label:"Show differences only",type:"bool",default_value:true},= {key:"show_counts",label:"Show summary counts",type:"bool",default_value:tr= ue},{key:"histogram_max",label:"Histogram maximum",type:"float",default_val= ue:null,help:"Clear value to set automatically"},{key:"mode",type:"string",= default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:functi= on(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear= ();this.track.request_draw()}});this.prefs=3Dthis.config.values;this.painte= r=3DL.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototyp= e,c.prototype);var d=3D{LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,C= ompositeTrack:f,DrawableGroup:P};var p=3Dfunction(ae,ad,ac){if("copy" in ae= ){return ae.copy(ac)}else{var af=3Dae.obj_type;if(!af){af=3Dae.track_type}r= eturn new d[af](ad,ac,ae)}};return{View:Y,DrawableGroup:P,LineTrack:h,Featu= reTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,ob= ject_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/tr= ackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filter= s"],function(ab,x,l,u,L,Y,i){var q=3Dab.extend;var V=3Dfunction(ac){return(= "isResolved" in ac)};var n=3D{};var k=3Dfunction(ac,ad){n[ac.attr("id")]=3D= ad};var m=3Dfunction(ac,ae,ag,af){ag=3D".group";var ad=3D{};n[ac.attr("id")= ]=3Daf;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an= =3D$(this),at=3D$(this).parent(),ak=3Dat.children(),am=3Dn[$(this).attr("id= ")],aj,ai,aq,ah,al;ai=3D$(this).parents(ag);if(ai.length!=3D=3D0){aq=3Dai.p= osition().top;ah=3Daq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefo= re(ai);var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_dr= awable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);= var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(= am);return}}}ai=3Dnull;for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));aq= =3Daj.position().top;ah=3Daq+aj.outerHeight();if(aj.is(ag)&&this!=3D=3Daj.g= et(0)&&ap.offsetY>=3Daq&&ap.offsetY<=3Dah){if(ap.offsetY-aq<ah-ap.offsetY){= aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(t= his)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add= _drawable(am);return}}for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));if(a= p.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass(= "intro"))){break}}if(al=3D=3D=3Dak.length){if(this!=3D=3Dak.get(al-1)){at.a= ppend(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!=3D=3Dak.ge= t(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(= ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=3Dac= .css("border-top");ad["border-bottom"]=3Dac.css("border-bottom");$(this).cs= s({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind(= "dragend",function(){$(this).css(ad)})};var aa=3D16,G=3D9,D=3D20,A=3D100,I= =3D12000,S=3D400,K=3D5000,w=3D100,o=3D"There was an error in indexing this = dataset. ",J=3D"A converter for this dataset is not installed. Please check= your datatypes_conf.xml file.",E=3D"No data for this chrom/contig.",v=3D"P= reparing data. This can take a while for a large dataset. If the visualizat= ion is saved and closed, preparation will continue in the background.",y=3D= "Tool cannot be rerun: ",a=3D"Loading data...",U=3D"Ready for display",Q=3D= 10,H=3D20;function W(ad,ac){if(!ac){ac=3D0}var ae=3DMath.pow(10,ac);return = Math.round(ad*ae)/ae}var r=3Dfunction(ad,ac,af){if(!r.id_counter){r.id_coun= ter=3D0}this.id=3Dr.id_counter++;this.name=3Daf.name;this.view=3Dad;this.co= ntainer=3Dac;this.config=3Dnew F({track:this,params:[{key:"name",label:"Nam= e",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:fun= ction(){this.track.set_name(this.track.config.values.name)}});this.prefs=3D= this.config.values;this.drag_handle_class=3Daf.drag_handle_class;this.is_ov= erview=3Dfalse;this.action_icons=3D{};this.content_visible=3Dtrue;this.cont= ainer_div=3Dthis.build_container_div();this.header_div=3Dthis.build_header_= div();if(this.header_div){this.container_div.append(this.header_div);this.i= cons_div=3D$("<div/>").css("float","left").hide().appendTo(this.header_div)= ;this.build_action_icons(this.action_icons_def);this.header_div.append($("<= div style=3D'clear: both'/>"));this.header_div.dblclick(function(ag){ag.sto= pPropagation()});var ae=3Dthis;this.container_div.hover(function(){ae.icons= _div.show()},function(){ae.icons_div.hide()});$("<div style=3D'clear: both'= />").appendTo(this.container_div)}};r.prototype.action_icons_def=3D[{name:"= toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:funct= ion(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle= -expand").removeClass("toggle");ac.hide_contents();ac.content_visible=3Dfal= se}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-= expand");ac.content_visible=3Dtrue;ac.show_contents()}}},{name:"settings_ic= on",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad= ){var af=3Dfunction(){hide_modal();$(window).unbind("keypress.check_enter_e= sc")},ac=3Dfunction(){ad.config.update_from_form($(".dialog-box"));hide_mod= al();$(window).unbind("keypress.check_enter_esc")},ae=3Dfunction(ag){if((ag= .keyCode||ag.which)=3D=3D=3D27){af()}else{if((ag.keyCode||ag.which)=3D=3D= =3D13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Co= nfigure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",ti= tle:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-toolti= p").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:functi= on(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content= _visible){return true}return false},request_draw:function(){},_draw:functio= n(){},to_dict:function(){},set_name:function(ac){this.old_name=3Dthis.name;= this.name=3Dac;this.name_div.text(this.name)},revert_name:function(){if(thi= s.old_name){this.name=3Dthis.old_name;this.name_div.text(this.name)}},remov= e:function(){this.changed();this.container.remove_drawable(this);var ac=3Dt= his.view;this.container_div.hide(0,function(){$(this).remove();ac.update_in= tro_div()})},build_container_div:function(){},build_header_div:function(){}= ,add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=3Dthis;this.action_icon= s[ad]=3D$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addCl= ass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendT= o(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:= function(ac){var ae;for(var ad=3D0;ad<ac.length;ad++){ae=3Dac[ad];this.add_= action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide= )}},update_icons:function(){},hide_contents:function(){},show_contents:func= tion(){},get_drawables:function(){}});var z=3Dfunction(ad,ac,ae){r.call(thi= s,ad,ac,ae);this.obj_type=3Dae.obj_type;this.drawables=3D[]};q(z.prototype,= r.prototype,{unpack_drawables:function(ae){this.drawables=3D[];var ad;for(v= ar ac=3D0;ac<ae.length;ac++){ad=3Dp(ae[ac],this.view,this);this.add_drawabl= e(ad)}},init:function(){for(var ac=3D0;ac<this.drawables.length;ac++){this.= drawables[ac].init()}},_draw:function(){for(var ac=3D0;ac<this.drawables.le= ngth;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=3D[];for(= var ac=3D0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dic= t())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawable= s:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=3Dthi= s;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad= =3Dthis.drawables.indexOf(ac);if(ad!=3D=3D-1){this.drawables.splice(ad,0,ae= );return true}return false},replace_drawable:function(ae,ac,ad){var af=3Dth= is.drawables.indexOf(ae);if(af!=3D=3D-1){this.drawables[af]=3Dac;if(ad){ae.= container_div.replaceWith(ac.container_div)}this.changed()}return af},remov= e_drawable:function(ad){var ac=3Dthis.drawables.indexOf(ad);if(ac!=3D=3D-1)= {this.drawables.splice(ac,1);ad.container=3Dnull;this.changed();return true= }return false},move_drawable:function(ad,ae){var ac=3Dthis.drawables.indexO= f(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);this.drawables.splice(ae,= 0,ad);this.changed();return true}return false},get_drawables:function(){ret= urn this.drawables}});var P=3Dfunction(ad,ac,af){q(af,{obj_type:"DrawableGr= oup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_= div=3D$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_cont= ent_div").appendTo(this.container_div);k(this.container_div,this);k(this.co= ntent_div,this);m(this.container_div,this.drag_handle_class,".group",this);= this.filters_manager=3Dnew i.FiltersManager(this);this.header_div.after(thi= s.filters_manager.parent_div);this.saved_filters_managers=3D[];if("drawable= s" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=3D= this.filters_manager;this.filters_manager=3Dnew i.FiltersManager(this,af.fi= lters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.fil= ters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototyp= e,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototyp= e.action_icons_def[1],{name:"composite_icon",title:"Show composite track",c= ss_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();= ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:= "filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac= .filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setu= p_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}= },r.prototype.action_icons_def[2]],build_container_div:function(){var ac=3D= $("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container= ){this.container.content_div.append(ac)}return ac},build_header_div:functio= n(){var ac=3D$("<div/>").addClass("track-header");ac.append($("<div/>").add= Class(this.drag_handle_class));this.name_div=3D$("<div/>").addClass("track-= name").text(this.name).appendTo(ac);return ac},hide_contents:function(){thi= s.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.req= uest_draw()},update_icons:function(){var ae=3Dthis.drawables.length;if(ae= =3D=3D=3D0){this.action_icons.composite_icon.hide();this.action_icons.filte= rs_icon.hide()}else{if(ae=3D=3D=3D1){if(this.drawables[0] instanceof f){thi= s.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}= else{var al,ak,ai,ao=3Dtrue,ag=3Dthis.drawables[0].get_type(),ac=3D0;for(al= =3D0;al<ae;al++){ai=3Dthis.drawables[al];if(ai.get_type()!=3D=3Dag){can_com= posite=3Dfalse;break}if(ai instanceof c){ac++}}if(ao||ac=3D=3D=3D1){this.ac= tion_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide= ();$(".bs-tooltip").remove()}if(ac>1&&ac=3D=3D=3Dthis.drawables.length){var= ap=3D{},ad;ai=3Dthis.drawables[0];for(ak=3D0;ak<ai.filters_manager.filters= .length;ak++){ad=3Dai.filters_manager.filters[ak];ap[ad.name]=3D[ad]}for(al= =3D1;al<this.drawables.length;al++){ai=3Dthis.drawables[al];for(ak=3D0;ak<a= i.filters_manager.filters.length;ak++){ad=3Dai.filters_manager.filters[ak];= if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();= var af,ah,aj,am;for(var an in ap){af=3Dap[an];if(af.length=3D=3D=3Dac){ah= =3Dnew i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_man= ager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_= icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{= this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function= (){for(var ac=3D0;ac<this.drawables.length;ac++){this.drawables[ac].filters= _manager=3Dthis.saved_filters_managers[ac]}this.saved_filters_managers=3D[]= },setup_multitrack_filtering:function(){if(this.filters_manager.filters.len= gth>0){this.saved_filters_managers=3D[];for(var ac=3D0;ac<this.drawables.le= ngth;ac++){drawable=3Dthis.drawables[ac];this.saved_filters_managers.push(d= 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s.overview_close.click(function(){ac.reset_overview()});this.viewport_conta= iner.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.wi= dth()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low= =3Dac.low;ah.current_height=3Dag.clientY;ah.current_x=3Dah.offsetX}).bind("= drag",function(ai,ak){var ag=3D$(this);var al=3Dak.offsetX-ak.current_x;var= ah=3Dag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.cur= rent_height=3Dai.clientY;ak.current_x=3Dak.offsetX;var aj=3DMath.round(al/a= c.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mo= usewheel",function(ai,ak,ah,ag){if(ah){ah*=3D50;var aj=3DMath.round(-ah/ac.= viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_= labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height= :ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltra= ck.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opaci= 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on(af){var ac=3Dthis;var ae=3Dac.high-ac.low;if(ac.low-af<ac.max_low){ac.lo= w=3Dac.max_low;ac.high=3Dac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.h= igh=3Dac.max_high;ac.low=3Dac.max_high-ae}else{ac.high-=3Daf;ac.low-=3Daf}}= ac.request_redraw();var ad=3Dac.chrom_select.val();this.trigger_navigate(ad= ,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.c= all(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_tr= ack:function(ac){ac.view=3Dthis;ac.init();this.label_tracks.push(ac)},remov= e_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad)= {var ac=3Dthis;ae.container_div.hide(0,function(){$(this).remove();ac.updat= e_intro_div()})}},reset:function(){this.low=3Dthis.max_low;this.high=3Dthis= .max_high;this.viewport_container.find(".yaxislabel").remove()},request_red= raw:function(ak,ac,aj,al){var ai=3Dthis,ah=3D(al?[al]:ai.drawables),ae;var = ad;for(var ag=3D0;ag<ah.length;ag++){ad=3Dah[ag];ae=3D-1;for(var af=3D0;af<= ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]=3D= =3D=3Dad){ae=3Daf;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}= else{ai.tracks_to_be_redrawn[ag][1]=3Dac;ai.tracks_to_be_redrawn[ag][2]=3Da= j}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(a= k)});this.requested_redraw=3Dtrue}},_redraw:function(am){this.requested_red= raw=3Dfalse;var aj=3Dthis.low,af=3Dthis.high;if(aj<this.max_low){aj=3Dthis.= max_low}if(af>this.max_high){af=3Dthis.max_high}var al=3Dthis.high-this.low= ;if(this.high!=3D=3D0&&al<this.min_separation){af=3Daj+this.min_separation}= this.low=3DMath.floor(aj);this.high=3DMath.ceil(af);this.update_location(th= is.low,this.high);this.resolution_b_px=3D(this.high-this.low)/this.viewport= _container.width();this.resolution_px_b=3Dthis.viewport_container.width()/(= this.high-this.low);var ac=3D(this.low/(this.max_high-this.max_low)*this.ov= erview_viewport.width())||0;var ai=3D((this.high-this.low)/(this.max_high-t= his.max_low)*this.overview_viewport.width())||0;var an=3D13;this.overview_b= ox.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.= css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highligh= t.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=3D0,ah=3Dthis.tra= cks_to_be_redrawn.length;ag<ah;ag++){ae=3Dthis.tracks_to_be_redrawn[ag][0];= ad=3Dthis.tracks_to_be_redrawn[ag][1];ak=3Dthis.tracks_to_be_redrawn[ag][2]= ;if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=3D[];for(ag=3D0,ah=3Dthi= s.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:= function(ad,ae){if(this.max_high=3D=3D=3D0||this.high-this.low<=3Dthis.min_= separation){return}var af=3Dthis.high-this.low,ag=3Daf/2+this.low,ac=3D(af/= this.zoom_factor)/2;if(ad){ag=3Dad/this.viewport_container.width()*(this.hi= gh-this.low)+this.low}this.low=3DMath.round(ag-ac);this.high=3DMath.round(a= g+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max= _high=3D=3D=3D0){return}var ad=3Dthis.high-this.low,ae=3Dad/2+this.low,ac= =3D(ad*this.zoom_factor)/2;this.low=3DMath.round(ae-ac);this.high=3DMath.ro= und(ae+ac);this.changed();this.request_redraw()},resize_window:function(){t= his.viewport_container.height(this.container.height()-this.top_container.he= ight()-this.bottom_container.height());this.request_redraw()},set_overview:= function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_i= d=3D=3D=3Dae.dataset_id){return}this.overview_viewport.find(".track").remov= e()}var ad=3Dae.copy({content_div:this.overview_viewport}),ac=3Dthis;ad.hea= der_div.hide();ad.is_overview=3Dtrue;ac.overview_drawable=3Dad;this.overvie= w_drawable.postdraw_actions=3Dfunction(){ac.overview_highlight.show().heigh= t(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac= .overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.o= verview_close.show();ac.resize_window()};ac.overview_drawable.request_draw(= 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s.filters_manager);this.filters_available=3Dfalse;this.tool=3D("tool" in af= &&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=3Dnew x.C= ache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);= if(this.tool){this.dynamic_tool_div=3Dthis.tool.parent_div;this.header_div.= after(this.dynamic_tool_div)}}this.tiles_div=3D$("<div/>").addClass("tiles"= ).appendTo(this.content_div);this.overlay_div=3D$("<div/>").addClass("overl= ay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M= .prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_ico= ns_def.concat([{name:"show_more_rows_icon",title:"To minimize track height,= not all feature rows are displayed. Click to display more rows.",css_class= :"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotte= rs[ac.view.resolution_px_b].max_rows*=3D2;ac.request_draw(true)},hide:true}= ]),copy:function(ac){var ad=3Dthis.to_dict();q(ad,{data_manager:this.data_m= anager});var ae=3Dnew this.constructor(this.view,ac,ad);ae.change_mode(this= .mode);ae.enabled=3Dthis.enabled;return ae},set_filters_manager:function(ac= ){this.filters_manager=3Dac;this.header_div.after(this.filters_manager.pare= nt_div)},to_dict:function(){return{track_type:this.get_type(),name:this.nam= e,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:t= his.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.= tool.state_dict():{})}},change_mode:function(ad){var ac=3Dthis;ac.mode=3Dad= ;ac.config.values.mode=3Dad;ac.tile_cache.clear();ac.request_draw();this.ac= tion_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");re= turn ac},update_icons:function(){var ac=3Dthis;if(ac.filters_available){ac.= action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}i= f(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_vi= z_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_= space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_= "+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad= ,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw= ()){return}var al=3Dthis.view.low,ah=3Dthis.view.high,aj=3Dah-al,ae=3Dthis.= view.container.width(),ap=3Dthis.view.resolution_px_b,ag=3Dthis.view.resolu= tion_b_px;if(this.is_overview){al=3Dthis.view.max_low;ah=3Dthis.view.max_hi= gh;ag=3D(view.max_high-view.max_low)/ae;ap=3D1/ag}this.before_draw();this.t= iles_div.children().addClass("remove");var ac=3DMath.floor(al/(ag*S)),ak=3D= true,ao=3D[],ai=3Dfunction(aq){return(aq&&"track" in aq)};while((ac*S*ag)<a= h){var am=3Dthis.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.p= ush(am)}else{ak=3Dfalse}ac+=3D1}if(!an){this.tiles_div.children(".remove").= removeClass("remove").remove()}var af=3Dthis;if(ak){this.tiles_div.children= (".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:fu= nction(ae,af,ah,ac){var ag=3Dfalse;for(var ad=3D0;ad<ae.length;ad++){if(ae[= ad].has_icons){ag=3Dtrue;break}}if(ag){for(var ad=3D0;ad<ae.length;ad++){ti= le=3Dae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw= _helper:function(ac,ao,au,ar,ah,ai,ap){var an=3Dthis,ax=3Dthis._gen_tile_ca= che_key(ao,ai,au),af=3Dthis._get_tile_bounds(au,ar);if(!ap){ap=3D{}}var aw= =3D(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,ah,ai);r= eturn aw}var al=3Dtrue;var at=3Dan.data_manager.get_data(af,an.mode,ar,an.d= ata_url_extra_params);if(V(at)){al=3Dfalse}var aj;if(view.reference_track&&= ai>view.canvas_manager.char_width_px){aj=3Dview.reference_track.data_manage= r.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(a= j)){al=3Dfalse}}if(al){q(at,ap.more_tile_data);var ak=3Dan.mode;if(ak=3D=3D= =3D"Auto"){ak=3Dan.get_mode(at);an.update_auto_mode(ak)}var ae=3Dan.view.ca= nvas_manager.new_canvas(),av=3Daf.get("start"),ad=3Daf.get("end"),ao=3DMath= .ceil((ad-av)*ai)+an.left_offset,am=3Dan.get_canvas_height(at,ak,ai,ao);ae.= width=3Dao;ae.height=3Dam;var aq=3Dae.getContext("2d");aq.translate(this.le= ft_offset,0);var aw=3Dan.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!=3D=3Dundefi= ned){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag= =3D$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,fal= se,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,= ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae)= {console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile= :function(ae,ah,ai){var ad=3Dthis,ac=3Dae.html_elt;ae.predisplay_actions();= var ag=3D(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(= this.left_offset){ag-=3Dthis.left_offset}ac.css({position:"absolute",top:0,= left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append= (ac)}ae.html_elt.height("auto");this.max_height_px=3DMath.max(this.max_heig= ht_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",th= is.max_height_px+"px");var af=3Dthis.max_height_px;if(this.visible_height_p= x!=3D=3D0){af=3DMath.min(this.max_height_px,this.visible_height_px)}this.ti= les_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=3DMa= th.floor(ac*S*ad),ag=3DMath.ceil(S*ad),ae=3D(af+ag<=3Dthis.view.max_high?af= +ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,st= art:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){var ad= =3Dthis,ag=3D(ae!=3D=3Dundefined&&ac!=3D=3Dundefined&&af!=3D=3Dundefined?ae= +":"+ac+"-"+af:"all");return" - region=3D["+ag+"], parameters=3D["+ad.tool.= get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad)= {return true},can_subset:function(ac){return false},init_for_tool_data:func= tion(){this.data_manager.set("data_type","raw_data");this.data_query_wait= =3D1000;this.dataset_check_type=3D"state";this.normal_postdraw_actions=3Dth= is.postdraw_actions;this.postdraw_actions=3Dfunction(ae,af,ah,ac){var ad=3D= this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type=3D"conve= rted_datasets_state";ad.data_query_wait=3DK;var ag=3Dnew l.ServerStateDefer= red({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda= :ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai= !=3D=3D"pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("da= ta_type","data")});ad.postdraw_actions=3Dad.normal_postdraw_actions}}});var= X=3Dfunction(ad,ac){var ae=3D{resize:false};g.call(this,ad,ac,ae);this.con= tainer_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header= _div:function(){},init:function(){this.enabled=3Dtrue},_draw:function(){var= ae=3Dthis.view,af=3Dae.high-ae.low,ai=3DMath.floor(Math.pow(10,Math.floor(= Math.log(af)/Math.log(10)))),ac=3DMath.floor(ae.low/ai)*ai,ag=3Dthis.view.c= ontainer.width(),ad=3D$("<div style=3D'position: relative; height: 1.3em;'>= </div>");while(ac<ae.high){var ah=3D(ac-ae.low)/af*ag;ad.append($("<div cla= ss=3D'label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1})= );ac+=3Dai}this.content_div.children(":first").remove();this.content_div.ap= pend(ad)}});var f=3Dfunction(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables= =3D[];this.left_offset=3D0;if("drawables" in ag){var af;for(var ae=3D0;ae<a= g.drawables.length;ae++){af=3Dag.drawables[ae];this.drawables[ae]=3Dp(af,ad= ,null);if(af.left_offset>this.left_offset){this.left_offset=3Daf.left_offse= t}}this.enabled=3Dtrue}if(this.drawables.length!=3D=3D0){this.set_display_m= odes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_ic= ons();this.obj_type=3D"CompositeTrack"};q(f.prototype,M.prototype,{action_i= cons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"= layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_gr= oup()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,a= dd_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_dr= awables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(= var ad=3D0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac= )}},init:function(){var ae=3D[];for(var ad=3D0;ad<this.drawables.length;ad+= +){ae.push(this.drawables[ad].init())}var ac=3Dthis;$.when.apply($,ae).then= (function(){ac.enabled=3Dtrue;ac.request_draw()})},update_icons:function(){= this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();t= his.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw= ,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=3Dthis,aD=3Dthis._gen_ti= le_cache_key(at,am,az),ah=3Dthis._get_tile_bounds(az,aw);if(!au){au=3D{}}va= r aC=3D(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC,ak,a= m);return aC}var al=3D[],ar,ap=3Dtrue,ax,an;for(var ay=3D0;ay<this.drawable= s.length;ay++){ar=3Dthis.drawables[ay];ax=3Dar.data_manager.get_data(ah,ar.= mode,aw,ar.data_url_extra_params);if(V(ax)){ap=3Dfalse}al.push(ax);an=3Dnul= l;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=3Dview.= reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_track.da= ta_url_extra_params);if(V(an)){ap=3Dfalse}}al.push(an)}if(ap){q(ax,au.more_= tile_data);this.tile_predraw_init();var ag=3Dar.view.canvas_manager.new_can= vas(),ai=3Dar._get_tile_bounds(az,aw),aA=3Dah.get("start"),ae=3Dah.get("end= "),aB=3D0,at=3DMath.ceil((ae-aA)*am)+this.left_offset,aq=3D0,af=3D[],ay;var= ac=3D0;for(ay=3D0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawabl= es[ay];ax=3Dal[aB];var ao=3Dar.mode;if(ao=3D=3D=3D"Auto"){ao=3Dar.get_mode(= ax);ar.update_auto_mode(ao)}af.push(ao);ac=3Dar.get_canvas_height(ax,ao,am,= at);if(ac>aq){aq=3Dac}}ag.width=3Dat;ag.height=3D(au.height?au.height:aq);a= B=3D0;var av=3Dag.getContext("2d");av.translate(this.left_offset,0);av.glob= alAlpha=3D0.5;av.globalCompositeOperation=3D"source-over";for(ay=3D0;ay<thi= s.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawables[ay];ax=3Dal[aB];an=3Da= l[aB+1];aC=3Dar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache.set_elt= (aD,aC);this.show_tile(aC,ak,am);return aC}var aj=3D$.Deferred(),ar=3Dthis;= $.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar= );aj.resolve()});return aj},show_group:function(){var af=3Dnew P(this.view,= this.container,{name:this.name}),ac;for(var ae=3D0;ae<this.drawables.length= ;ae++){ac=3Dthis.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.con= tainer=3Daf;af.content_div.append(ac.container_div)}var ad=3Dthis.container= .replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:functi= on(){var af=3DNumber.MAX_VALUE,ac=3D-af,ad;for(var ae=3D0;ae<this.drawables= .length;ae++){ad=3Dthis.drawables[ae];if(ad instanceof h){if(ad.prefs.min_v= alue<af){af=3Dad.prefs.min_value}if(ad.prefs.max_value>ac){ac=3Dad.prefs.ma= x_value}}}for(var ae=3D0;ae<this.drawables.length;ae++){ad=3Dthis.drawables= [ae];ad.prefs.min_value=3Daf;ad.prefs.max_value=3Dac}},postdraw_actions:fun= ction(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var = ag=3D-1;for(var af=3D0;af<ae.length;af++){var ac=3Dae[af].html_elt.find("ca= nvas").height();if(ac>ag){ag=3Dac}}for(var af=3D0;af<ae.length;af++){var ai= =3Dae[af];if(ai.html_elt.find("canvas").height()!=3D=3Dag){this.draw_helper= (true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.htm= l_elt.remove()}}}});var B=3Dfunction(ac){M.call(this,ac,{content_div:ac.top= _labeltrack},{resize:false});ac.reference_track=3Dthis;this.left_offset=3D2= 00;this.visible_height_px=3D12;this.container_div.addClass("reference-track= ");this.content_div.css("background","none");this.content_div.css("min-heig= ht","0px");this.content_div.css("border","none");this.data_url=3Dreference_= url+"/"+this.view.dbkey;this.data_url_extra_params=3D{reference:true};this.= data_manager=3Dnew x.ReferenceTrackDataManager({data_url:this.data_url});th= is.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div= :function(){},init:function(){this.data_manager.clear();this.enabled=3Dtrue= },can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah,ai,af){= if(ai>this.view.canvas_manager.char_width_px){return M.prototype.draw_helpe= r.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return null}},d= raw_tile:function(ak,al,ag,af,ai,am){var ae=3Dthis;if(am>this.view.canvas_m= anager.char_width_px){if(ak.data=3D=3D=3Dnull){this.hide_contents();return}= var ad=3Dal.canvas;al.font=3Dal.canvas.manager.default_font;al.textAlign=3D= "center";ak=3Dak.data;for(var ah=3D0,aj=3Dak.length;ah<aj;ah++){var ac=3DMa= th.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();return new b= (ae,ai,af,ad,ak)}this.hide_contents()}});var h=3Dfunction(ae,ad,af){var ac= =3Dthis;this.display_modes=3D["Histogram","Line","Filled","Intensity"];this= .mode=3D"Histogram";M.call(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.= dataset_id=3Daf.dataset_id;this.original_dataset_id=3Dthis.dataset_id;this.= left_offset=3D0;this.config=3Dnew F({track:this,params:[{key:"name",label:"= Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:= "color",default_value:l.get_random_color()},{key:"min_value",label:"Min Val= ue",type:"float",default_value:undefined},{key:"max_value",label:"Max Value= ",type:"float",default_value:undefined},{key:"mode",type:"string",default_v= alue:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidde= n:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.nam= e);ac.vertical_range=3Dac.prefs.max_value-ac.prefs.min_value;ac.set_min_val= ue(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs= =3Dthis.config.values;this.visible_height_px=3Dthis.config.values.height;th= is.vertical_range=3Dthis.config.values.max_value-this.config.values.min_val= ue};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.reques= t_draw(true)},set_min_value:function(ac){this.prefs.min_value=3Dac;$("#line= track_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cac= he.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_v= alue=3Dac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_va= lue);this.tile_cache.clear();this.request_draw()},predraw_init:function(){v= ar ac=3Dthis;ac.vertical_range=3Dundefined;return $.getJSON(ac.dataset.url(= ),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_h= igh,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-trac= k");var ag=3Dad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseF= loat(ac.prefs.max_value))){var ae=3Dag.min,ai=3Dag.max;ae=3DMath.floor(Math= .min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=3DMath.ceil(Math.max(0,Math.min(ai= ,ag.mean+2*ag.sd)));ac.prefs.min_value=3Dae;ac.prefs.max_value=3Dai;$("#tra= ck_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.datase= t_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=3Dac.prefs.max_va= lue-ac.prefs.min_value;ac.total_frequency=3Dag.total_frequency;ac.container= _div.find(".yaxislabel").remove();var ah=3D$("<div/>").text(W(ac.prefs.min_= value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tool= tip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}= },help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","line= track_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=3D$("<div/>= ").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:f= unction(aj){$(".bs-tooltip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)= ){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel t= op").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container= _div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=3Daj.canvas,af=3Dag.g= et("start"),ai=3Dag.get("end"),ah=3Dnew L.LinePainter(al.data,af,ai,this.pr= efs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.dat= a)},can_subset:function(ac){return false}});var t=3Dfunction(ae,ad,af){var = ac=3Dthis;this.display_modes=3D["Heatmap"];this.mode=3D"Heatmap";M.call(thi= s,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.dataset_id=3Daf.dataset_id;thi= s.original_dataset_id=3Dthis.dataset_id;this.left_offset=3D0;this.config=3D= new F({track:this,params:[{key:"name",label:"Name",type:"text",default_valu= e:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_v= alue:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",defaul= t_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_= value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},= {key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height= ",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange= :function(){ac.set_name(ac.prefs.name);ac.vertical_range=3Dac.prefs.max_val= ue-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value= (ac.prefs.max_value)}});this.prefs=3Dthis.config.values;this.visible_height= _px=3Dthis.config.values.height;this.vertical_range=3Dthis.config.values.ma= x_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype= ,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){= this.prefs.min_value=3Dac;this.tile_cache.clear();this.request_draw()},set_= max_value:function(ac){this.prefs.max_value=3Dac;this.tile_cache.clear();th= is.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=3Dae.canvas= ,ad=3Dnew L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),th= is.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,a= c.data)}});var c=3Dfunction(af,ae,ah){var ad=3Dthis;this.display_modes=3D["= Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=3Dl.= get_random_color(),ac=3Dl.get_random_color([ag,"#FFFFFF"]);this.config=3Dne= w F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:= this.name},{key:"block_color",label:"Block color",type:"color",default_valu= e:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"colo= r",default_value:ac},{key:"label_color",label:"Label color",type:"color",de= fault_value:"black"},{key:"show_counts",label:"Show summary counts",type:"b= ool",default_value:true,help:"Show the number of items in each bin when dra= wing summary histogram"},{key:"histogram_max",label:"Histogram maximum",typ= e:"float",default_value:null,help:"clear value to set automatically"},{key:= "connector_style",label:"Connector style",type:"select",default_value:"fish= bones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",v= alue:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:tru= e},{key:"height",type:"int",default_value:this.visible_height_px,hidden:tru= e}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad= .tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.= prefs=3Dthis.config.values;this.visible_height_px=3Dthis.config.values.heig= ht;this.container_div.addClass("feature-track");this.hda_ldda=3Dah.hda_ldda= ;this.dataset_id=3Dah.dataset_id;this.original_dataset_id=3Dah.dataset_id;t= his.show_labels_scale=3D0.001;this.showing_details=3Dfalse;this.summary_dra= w_height=3D30;this.slotters=3D{};this.start_end_dct=3D{};this.left_offset= =3D200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototyp= e,{set_dataset:function(ac){this.dataset_id=3Dac.get("id");this.hda_ldda=3D= ac.get("hda_ldda");this.dataset=3Dac;this.data_manager.set("dataset",ac)},s= et_painter_from_config:function(){if(this.config.values.connector_style=3D= =3D=3D"arcs"){this.painter=3DL.ArcLinkedFeaturePainter}else{this.painter=3D= L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=3D0},pos= tdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,= ar,ag);var al=3Dthis,ao;if(al.mode=3D=3D=3D"Coverage"){var ad=3D-1;for(ao= =3D0;ao<ar.length;ao++){var an=3Dar[ao].max_val;if(an>ad){ad=3Dan}}for(ao= =3D0;ao<ar.length;ao++){var au=3Dar[ao];if(au.max_val!=3D=3Dad){au.html_elt= .remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(= ),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=3Dal.filter= s_manager.filters;for(var aq=3D0;aq<ai.length;aq++){ai[aq].update_ui_elt()}= var at=3Dfalse,ac,aj;for(ao=3D0;ao<ar.length;ao++){if(ar[ao].data.length){a= c=3Dar[ao].data[0];for(var aq=3D0;aq<ai.length;aq++){aj=3Dai[aq];if(aj.appl= ies_to(ac)&&aj.min!=3D=3Daj.max){at=3Dtrue;break}}}}if(al.filters_available= !=3D=3Dat){al.filters_available=3Dat;if(!al.filters_available){al.filters_m= anager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").rem= ove();var af=3Dar[0];if(af instanceof j){var ak=3D(this.prefs.histogram_max= ?this.prefs.histogram_max:af.max_val),ae=3D$("<div/>").text(ak).make_text_e= ditable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var a= v=3DparseFloat(av);al.prefs.histogram_max=3D(!isNaN(av)?av:null);al.tile_ca= che.clear();al.request_draw()},help_text:"Set max value; leave blank to use= default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);= this.container_div.prepend(ae)}if(af instanceof O){var ap=3Dtrue;for(ao=3D0= ;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=3Dfalse;break}}if(!ap){this.= action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_ro= ws_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_= auto_mode:function(ac){var ac;if(this.mode=3D=3D=3D"Auto"){if(ac=3D=3D=3D"n= o_detail"){ac=3D"feature spans"}else{if(ac=3D=3D=3D"summary_tree"){ac=3D"co= verage histogram"}}this.action_icons.mode_icon.attr("title","Set display mo= de (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=3Dthi= s.view.canvas_manager.dummy_context,ae=3Dthis.slotters[ag];if(!ae||(ae.mode= !=3D=3Daf)){ae=3Dnew (u.FeatureSlotter)(ag,af,A,function(ah){return ad.meas= ureText(ah)});this.slotters[ag]=3Dae}return ae.slot_features(ac)},get_mode:= function(ac){if(ac.dataset_type=3D=3D=3D"summary_tree"){mode=3D"summary_tre= e"}else{if(ac.extra_info=3D=3D=3D"no_detail"||this.is_overview){mode=3D"no_= detail"}else{if(this.view.high-this.view.low>I){mode=3D"Squish"}else{mode= =3D"Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag=3D= =3D=3D"summary_tree"||ag=3D=3D=3D"Coverage"){return this.summary_draw_heigh= t}else{var af=3Dthis.incremental_slots(ah,ac.data,ag);var ae=3Dnew (this.pa= inter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_hei= ght(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=3Dthis,ad=3Da= q.canvas,ay=3Daf.get("start"),ac=3Daf.get("end"),ag=3Dthis.left_offset;if(a= o=3D=3D=3D"summary_tree"||ao=3D=3D=3D"Coverage"){var aA=3Dnew L.SummaryTree= Painter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j= (ap,af,ar,ad,am.data,am.max)}var ai=3D[],an=3Dthis.slotters[aj].slots;all_s= lotted=3Dtrue;if(am.data){var ak=3Dthis.filters_manager.filters;for(var at= =3D0,av=3Dam.data.length;at<av;at++){var ah=3Dam.data[at];var au=3Dfalse;va= r al;for(var ax=3D0,aC=3Dak.length;ax<aC;ax++){al=3Dak[ax];al.update_attrs(= ah);if(!al.keep(ah)){au=3Dtrue;break}}if(!au){ai.push(ah);if(!(ah[0] in an)= ){all_slotted=3Dfalse}}}}var aB=3D(this.filters_manager.alpha_filter?new C(= this.filters_manager.alpha_filter):null);var az=3D(this.filters_manager.hei= ght_filter?new C(this.filters_manager.height_filter):null);var aA=3Dnew (th= is.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=3Dnull;aq.fillStyle=3Dt= his.prefs.block_color;aq.font=3Daq.canvas.manager.default_font;aq.textAlign= =3D"right";if(am.data){aw=3DaA.draw(aq,ad.width,ad.height,aj,an);aw.transla= tion=3D-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw= )},data_and_mode_compatible:function(ac,ad){if(ad=3D=3D=3D"Auto"){return tr= ue}else{if(ad=3D=3D=3D"Coverage"){return ac.dataset_type=3D=3D=3D"summary_t= ree"}else{if(ac.extra_info=3D=3D=3D"no_detail"||ac.dataset_type=3D=3D=3D"su= mmary_tree"){return false}else{return true}}}},can_subset:function(ac){if(a= c.dataset_type=3D=3D=3D"summary_tree"||ac.message||ac.extra_info=3D=3D=3D"n= o_detail"){return false}return true}});var R=3Dfunction(ad,ac,ae){c.call(th= is,ad,ac,ae);this.config=3Dnew F({track:this,params:[{key:"name",label:"Nam= e",type:"text",default_value:this.name},{key:"block_color",label:"Block col= or",type:"color",default_value:l.get_random_color()},{key:"label_color",lab= el:"Label color",type:"color",default_value:"black"},{key:"show_insertions"= ,label:"Show insertions",type:"bool",default_value:false},{key:"show_counts= ",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",t= ype:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,on= change:function(){this.track.set_name(this.track.prefs.name);this.track.til= e_cache.clear();this.track.request_draw()}});this.prefs=3Dthis.config.value= s;this.painter=3DL.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.pro= totype);var T=3Dfunction(ae,ad,ag){c.call(this,ae,ad,ag);var af=3Dl.get_ran= dom_color(),ac=3Dl.get_random_color([af,"#ffffff"]);this.config=3Dnew F({tr= ack:this,params:[{key:"name",label:"Name",type:"text",default_value:this.na= me},{key:"block_color",label:"Block and sense strand color",type:"color",de= fault_value:af},{key:"reverse_strand_color",label:"Antisense strand color",= type:"color",default_value:ac},{key:"label_color",label:"Label color",type:= "color",default_value:"black"},{key:"show_insertions",label:"Show insertion= s",type:"bool",default_value:false},{key:"show_differences",label:"Show dif= ferences only",type:"bool",default_value:true},{key:"show_counts",label:"Sh= ow summary counts",type:"bool",default_value:true},{key:"histogram_max",lab= el:"Histogram maximum",type:"float",default_value:null,help:"Clear value to= set automatically"},{key:"mode",type:"string",default_value:this.mode,hidd= en:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(thi= s.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()= }});this.prefs=3Dthis.config.values;this.painter=3DL.ReadPainter;this.updat= e_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d=3D{Line= Track:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,Compos= iteTrack:f,DrawableGroup:P};var p=3Dfunction(ae,ad,ac){if("copy" in ae){ret= urn ae.copy(ac)}else{var af=3Dae.obj_type;if(!af){af=3Dae.track_type}return= new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,F= eatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:= f,object_from_template:p}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/p= ainters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){= var a=3Db.object_from_template;var f=3Dg.Base.extend({initialize:function(j= ){this.baseURL=3Dj},createButtonMenu:function(){var j=3Dthis,k=3Dcreate_ico= n_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:funct= ion(){d.select_datasets(select_datasets_url,add_track_async_url,view.dbkey,= function(l){c.each(l,function(m){view.add_drawable(a(m,view,view))})})}},{i= con_class:"block--plus",title:"Add group",on_click:function(){view.add_draw= able(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"book= marks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("d= iv#right").css("right")=3D=3D"0px"?"hide":"show"))}},{icon_class:"globe",ti= tle:"Circster",on_click:function(){window.location=3Dj.baseURL+"visualizati= on/circster?id=3D"+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_= click:function(){show_modal("Saving...","progress");var l=3D[];$(".bookmark= ").each(function(){l.push({position:$(this).children(".position").text(),an= notation:$(this).children(".annotation").text()})});var m=3D(view.overview_= drawable?view.overview_drawable.name:null),n=3D{view:view.to_dict(),viewpor= t:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bookmarks:l};$= .ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json= ",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vi= s_json:JSON.stringify(n)}}).success(function(o){hide_modal();view.vis_id=3D= o.vis_id;view.has_changes=3Dfalse;window.history.pushState({},"",o.url+wind= ow.location.hash)}).error(function(){show_modal("Could Not Save","Could not= save visualization. Please try again later.",{Close:hide_modal})})}},{icon= _class:"cross-circle",title:"Close",on_click:function(){window.location=3Dj= .baseURL+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});thi= s.buttonMenu=3Dk;return k},add_bookmarks:function(){var j=3Dthis,k=3Dthis.b= aseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({ur= l:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},= error:function(){alert("Grid failed")},success:function(l){show_modal("Sele= ct dataset for new bookmarks",l,{Cancel:function(){hide_modal()},Insert:fun= ction(){$("input[name=3Did]:checked,input[name=3Dldda_ids]:checked").first(= ).each(function(){var m,n=3D$(this).val();if($(this).attr("name")=3D=3D=3D"= id"){m=3D{hda_id:n}}else{m=3D{ldda_id:n}}$.ajax({url:this.baseURL+"/visuali= zation/bookmarks_from_dataset",data:m,dataType:"json"}).then(function(o){fo= r(i=3D0;i<o.data.length;i++){var p=3Do.data[i];j.add_bookmark(p[0],p[1])}})= });hide_modal()}})}})},add_bookmark:function(n,l,j){var p=3D$("#bookmarks-c= ontainer"),r=3D$("<div/>").addClass("bookmark").appendTo(p);var s=3D$("<div= />").addClass("position").appendTo(r),o=3D$("<a href=3D''/>").text(n).appen= dTo(s).click(function(){view.go_to(n);return false}),m=3D$("<div/>").text(l= ).appendTo(r);if(j){var q=3D$("<div/>").addClass("delete-icon-container").p= rependTo(r).click(function(){r.slideUp("fast");r.remove();view.has_changes= =3Dtrue;return false}),k=3D$("<a href=3D''/>").addClass("icon-button delete= ").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:true,help_text= :"Edit bookmark note"}).addClass("annotation")}view.has_changes=3Dtrue;retu= rn r},create_visualization:function(o,j,n,p,m){var l=3Dthis,k=3Dnew b.View(= o);k.editor=3Dtrue;$.when(k.load_chroms_deferred).then(function(){if(j){var= y=3Dj.chrom,q=3Dj.start,v=3Dj.end,s=3Dj.overview;if(y&&(q!=3D=3Dundefined)= &&v){k.change_chrom(y,q,v)}}if(n){var t,r,u;for(var w=3D0;w<n.length;w++){k= .add_drawable(a(n[w],k,k))}}k.update_intro_div();var z;for(var w=3D0;w<k.dr= awables.length;w++){if(k.drawables[w].name=3D=3D=3Ds){k.set_overview(k.draw= ables[w]);break}}if(p){var x;for(var w=3D0;w<p.length;w++){x=3Dp[w];l.add_b= ookmark(x.position,x.annotation,m)}}k.has_changes=3Dfalse});return k},init_= keyboard_nav:function(j){$(document).keydown(function(k){if($(k.srcElement)= .is(":input")){return}switch(k.which){case 37:j.move_fraction(0.25);break;c= ase 38:var l=3DMath.round(j.viewport_container.height()/15);j.viewport_cont= ainer.scrollTop(j.viewport_container.scrollTop()-20);break;case 39:j.move_f= raction(-0.25);break;case 40:var l=3DMath.round(j.viewport_container.height= ()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()+20);= break}})}});return{object_from_template:a,TracksterUI:f}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/p= ainters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){= var a=3Db.object_from_template;var f=3Dg.Base.extend({initialize:function(j= ){this.baseURL=3Dj},createButtonMenu:function(){var j=3Dthis,k=3Dcreate_ico= n_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:funct= ion(){d.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":= view.dbkey},function(l){c.each(l,function(m){view.add_drawable(a(m,view,vie= w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){v= iew.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon= _class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right= _panel(($("div#right").css("right")=3D=3D"0px"?"hide":"show"))}},{icon_clas= s:"globe",title:"Circster",on_click:function(){window.location=3Dj.baseURL+= "visualization/circster?id=3D"+view.vis_id}},{icon_class:"disk--arrow",titl= e:"Save",on_click:function(){show_modal("Saving...","progress");var l=3D[];= $(".bookmark").each(function(){l.push({position:$(this).children(".position= ").text(),annotation:$(this).children(".annotation").text()})});var m=3D(vi= ew.overview_drawable?view.overview_drawable.name:null),n=3D{view:view.to_di= ct(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bo= okmarks:l};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",da= taType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"t= rackster",vis_json:JSON.stringify(n)}}).success(function(o){hide_modal();vi= ew.vis_id=3Do.vis_id;view.has_changes=3Dfalse;window.history.pushState({},"= ",o.url+window.location.hash)}).error(function(){show_modal("Could Not Save= ","Could not save visualization. Please try again later.",{Close:hide_modal= })})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.= location=3Dj.baseURL+"visualization/list"}}],{tooltip_config:{placement:"bo= ttom"}});this.buttonMenu=3Dk;return k},add_bookmarks:function(){var j=3Dthi= s,k=3Dthis.baseURL;show_modal("Select dataset for new bookmarks","progress"= );$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":= view.dbkey},error:function(){alert("Grid failed")},success:function(l){show= _modal("Select dataset for new bookmarks",l,{Cancel:function(){hide_modal()= },Insert:function(){$("input[name=3Did]:checked,input[name=3Dldda_ids]:chec= ked").first().each(function(){var m,n=3D$(this).val();if($(this).attr("name= ")=3D=3D=3D"id"){m=3D{hda_id:n}}else{m=3D{ldda_id:n}}$.ajax({url:this.baseU= RL+"/visualization/bookmarks_from_dataset",data:m,dataType:"json"}).then(fu= nction(o){for(i=3D0;i<o.data.length;i++){var p=3Do.data[i];j.add_bookmark(p= [0],p[1])}})});hide_modal()}})}})},add_bookmark:function(n,l,j){var p=3D$("= #bookmarks-container"),r=3D$("<div/>").addClass("bookmark").appendTo(p);var= s=3D$("<div/>").addClass("position").appendTo(r),o=3D$("<a href=3D''/>").t= ext(n).appendTo(s).click(function(){view.go_to(n);return false}),m=3D$("<di= v/>").text(l).appendTo(r);if(j){var q=3D$("<div/>").addClass("delete-icon-c= ontainer").prependTo(r).click(function(){r.slideUp("fast");r.remove();view.= has_changes=3Dtrue;return false}),k=3D$("<a href=3D''/>").addClass("icon-bu= tton delete").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:tru= e,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes= =3Dtrue;return r},create_visualization:function(o,j,n,p,m){var l=3Dthis,k= =3Dnew b.TracksterView(o);k.editor=3Dtrue;$.when(k.load_chroms_deferred).th= en(function(){if(j){var y=3Dj.chrom,q=3Dj.start,v=3Dj.end,s=3Dj.overview;if= (y&&(q!=3D=3Dundefined)&&v){k.change_chrom(y,q,v)}}if(n){var t,r,u;for(var = w=3D0;w<n.length;w++){k.add_drawable(a(n[w],k,k))}}k.update_intro_div();var= z;for(var w=3D0;w<k.drawables.length;w++){if(k.drawables[w].name=3D=3D=3Ds= ){k.set_overview(k.drawables[w]);break}}if(p){var x;for(var w=3D0;w<p.lengt= h;w++){x=3Dp[w];l.add_bookmark(x.position,x.annotation,m)}}k.has_changes=3D= false});return k},init_keyboard_nav:function(j){$(document).keydown(functio= n(k){if($(k.srcElement).is(":input")){return}switch(k.which){case 37:j.move= _fraction(0.25);break;case 38:var l=3DMath.round(j.viewport_container.heigh= t()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()-20)= ;break;case 39:j.move_fraction(-0.25);break;case 40:var l=3DMath.round(j.vi= ewport_container.height()/15);j.viewport_container.scrollTop(j.viewport_con= tainer.scrollTop()+20);break}})}});return{object_from_template:a,TracksterU= I:f}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],= function(s,i,l,p){var a=3Dfunction(u,x,v,w){$.ajax({url:u,data:(v?{"f-dbkey= ":v}:{}),error:function(){alert("Grid failed")},success:function(y){show_mo= dal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add= :function(){var z=3D[];$("input[name=3Did]:checked,input[name=3Dldda_ids]:c= hecked").each(function(){var A=3D{data_type:"track_config",hda_ldda:"hda"},= B=3D$(this).val();if($(this).attr("name")!=3D=3D"id"){A.hda_ldda=3D"ldda"}z= [z.length]=3D$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,= z).then(function(){var A=3D(arguments[0] instanceof Array?$.map(arguments,f= unction(B){return B[0]}):[arguments[0]]);w(A)});hide_modal()}})}})};var j= =3Dfunction(u){return("isResolved" in u)};var f=3Dfunction(u){this.default_= font=3Du!=3D=3Dundefined?u:"9px Monaco, Lucida Console, monospace";this.dum= my_canvas=3Dthis.new_canvas();this.dummy_context=3Dthis.dummy_canvas.getCon= text("2d");this.dummy_context.font=3Dthis.default_font;this.char_width_px= =3Dthis.dummy_context.measureText("A").width;this.patterns=3D{};this.load_p= attern("right_strand","/visualization/strand_right.png");this.load_pattern(= "left_strand","/visualization/strand_left.png");this.load_pattern("right_st= rand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_st= rand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load= _pattern:function(u,y){var v=3Dthis.patterns,w=3Dthis.dummy_context,x=3Dnew= Image();x.src=3Dgalaxy_paths.attributes.image_path+y;x.onload=3Dfunction()= {v[u]=3Dw.createPattern(x,"repeat")}},get_pattern:function(u){return this.p= atterns[u]},new_canvas:function(){var u=3D$("<canvas/>")[0];if(window.G_vml= CanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=3Dthis;return u}= });var q=3DBackbone.Model.extend({defaults:{num_elements:20,obj_cache:null,= key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var = w=3Dthis.attributes.obj_cache,x=3Dthis.attributes.key_ary,u=3Dx.indexOf(v);= if(u!=3D=3D-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_= to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=3Dthis.attributes.obj= _cache,z=3Dthis.attributes.key_ary,w=3Dthis.attributes.num_elements;if(!y[v= ]){if(z.length>=3Dw){var u=3Dz.shift();delete y[u]}z.push(v)}y[v]=3Dx;retur= n x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this= .attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache=3D{= };this.attributes.key_ary=3D[]},size:function(){return this.attributes.key_= ary.length}});var d=3Dq.extend({defaults:s.extend({},q.prototype.defaults,{= dataset:null,init_data:null,filters_manager:null,data_type:"data",data_mode= _compatible:function(u,v){return true},can_subset:function(u){return false}= }),initialize:function(u){q.prototype.initialize.call(this);var v=3Dthis.ge= t("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("n= um_elements")<u.length){this.set("num_elements",u.length)}var v=3Dthis;s.ea= ch(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x= =3Dthis.get("dataset"),w=3D$.Deferred(),u=3D(this.get("data_type")=3D=3D"ra= w_data"?"state":this.get("data_type")=3D=3D"data"?"converted_datasets_state= ":"error"),v=3Dnew l.ServerStateDeferred({ajax_settings:{url:this.get("data= set").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},= interval:5000,success_fn:function(y){return y!=3D=3D"pending"}});$.when(v.g= o()).then(function(y){w.resolve(y=3D=3D=3D"ok"||y=3D=3D=3D"data")});return = w},search_features:function(u){var v=3Dthis.get("dataset"),w=3D{query:u,hda= _ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},= load_data:function(C,B,v,A){var y=3Dthis.get("dataset"),x=3D{data_type:this= .get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end")= ,mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=3Dthis= .get("filters_manager");if(E){var F=3D[];var u=3DE.filters;for(var z=3D0;z<= u.length;z++){F.push(u[z].name)}x.filter_cols=3DJSON.stringify(F)}var w=3Dt= his,D=3D$.getJSON(y.url(),x,function(G){w.set_data(C,G)});this.set_data(C,D= );return D},get_data:function(A,z,w,y){var B=3Dthis.get_elt(A);if(B&&(j(B)|= |this.get("data_mode_compatible")(B,z))){return B}var C=3Dthis.get("key_ary= "),v=3Dthis.get("obj_cache"),D,u;for(var x=3D0;x<C.length;x++){D=3DC[x];u= =3Dnew g({from_str:D});if(u.contains(A)){B=3Dv[D];if(j(B)||(this.get("data_= mode_compatible")(B,z)&&this.get("can_subset")(B))){this.move_key_to_end(D,= x);return B}}}return this.load_data(A,z,w,y)},set_data:function(v,u){this.s= et_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:fu= nction(C,B,x,A,y){var E=3Dthis._mark_stale(C);if(!(E&&this.get("data_mode_c= ompatible")(E,B))){console.log("ERROR: problem with getting more data: curr= ent data is not compatible");return}var w=3DC.get("start");if(y=3D=3D=3Dthi= s.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y=3D=3D=3D= this.BROAD_DATA_REQ){w=3D(E.max_high?E.max_high:E.data[E.data.length-1][2])= +1}}var D=3DC.copy().set("start",w);var v=3Dthis,z=3Dthis.load_data(D,B,x,A= ),u=3D$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data)= {F.data=3DE.data.concat(F.data);if(F.max_low){F.max_low=3DE.max_low}if(F.me= ssage){F.message=3DF.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,= F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=3D= this.get_elt(v);return(u.dataset_type=3D=3D=3D"bigwig"&&u.data.length<8000)= },get_more_detailed_data:function(x,z,v,y,w){var u=3Dthis._mark_stale(x);if= (!u){console.log("ERROR getting more detailed data: no current data");retur= n}if(!w){w=3D{}}if(u.dataset_type=3D=3D=3D"bigwig"){w.num_samples=3D1000*y}= else{if(u.dataset_type=3D=3D=3D"summary_tree"){w.level=3DMath.min(u.level-1= ,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=3Dthis.g= et_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("= dataset"),v.toString())}u.stale=3Dtrue;return u},get_genome_wide_data:funct= ion(u){var w=3Dthis,y=3Dtrue,x=3Ds.map(u.get("chroms_info").chrom_info,func= tion(A){var z=3Dw.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){= y=3Dfalse}return z});if(y){return x}var v=3D$.Deferred();$.getJSON(this.get= ("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);= v.resolve(z.data)});return v},get_elt:function(u){return q.prototype.get_el= t.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt= .call(this,v.toString(),u)}});var n=3Dd.extend({initialize:function(u){var = v=3Dnew Backbone.Model();v.urlRoot=3Du.data_url;this.set("dataset",v)},load= _data:function(w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_d= ata.call(this,w,x,u,v)}});var c=3DBackbone.Model.extend({defaults:{name:nul= l,key:null,chroms_info:null},initialize:function(u){this.id=3Du.dbkey},get_= chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_c= hrom_region:function(u){var v=3Ds.find(this.get_chroms_info(),function(w){r= eturn w.chrom=3D=3Du});return new g({chrom:v.chrom,end:v.len})}});var g=3DB= ackbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHRO= MS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTA= INED_BY:1005,AFTER:1006},initialize:function(v){if(v.from_str){var x=3Dv.fr= om_str.split(":"),w=3Dx[0],u=3Dx[1].split("-");this.set({chrom:w,start:pars= eInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom= :this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:fu= nction(){return this.get("end")-this.get("start")},toString:function(){retu= rn this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:func= tion(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get(= "end")}},compute_overlap:function(B){var v=3Dthis.get("chrom"),A=3DB.get("c= hrom"),z=3Dthis.get("start"),x=3DB.get("start"),y=3Dthis.get("end"),w=3DB.g= et("end"),u;if(v&&A&&v!=3D=3DA){return this.get("DIF_CHROMS")}if(z<x){if(y<= x){u=3Dthis.get("BEFORE")}else{if(y<=3Dw){u=3Dthis.get("OVERLAP_START")}els= e{u=3Dthis.get("CONTAINS")}}}else{if(z>w){u=3Dthis.get("AFTER")}else{if(y<= =3Dw){u=3Dthis.get("CONTAINED_BY")}else{u=3Dthis.get("OVERLAP_END")}}}retur= n u},contains:function(u){return this.compute_overlap(u)=3D=3D=3Dthis.get("= CONTAINS")},overlaps:function(u){return s.intersection([this.compute_overla= p(u)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length= =3D=3D=3D0}});var m=3DBackbone.Collection.extend({model:g});var e=3DBackbon= e.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:B= ackbone.HasOne,key:"region",relatedModel:g}]});var r=3DBackbone.Collection.= extend({model:e});var t=3Di.Dataset.extend({initialize:function(u){this.set= ("id",u.dataset_id);this.set("config",p.ConfigSettingCollection.from_config= _dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")}= ,{key:"color"}]);var v=3Dthis.get("preloaded_data");if(v){v=3Dv.data}else{v= =3D[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var o= =3DBackbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_= paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(= ),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var= k=3Do.extend({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:n= ull,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"t= racks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}})= ;var b=3DBackbone.Model.extend({});var h=3DBackbone.Router.extend({initiali= ze:function(v){this.view=3Dv.view;this.route(/([\w]+)$/,"change_location");= this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=3Dthis;u.view= .on("navigate",function(w){u.navigate(w)})},change_location:function(u){thi= s.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmark= Collection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeReg= ion:g,GenomeRegionCollection:m,GenomeVisualization:k,ReferenceTrackDataMana= ger:n,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}= }); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],= function(s,i,l,p){var a=3Dfunction(u,x,w,v){$.ajax({url:u,data:w,error:func= tion(){alert("Grid failed")},success:function(y){show_modal("Select dataset= s for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z= =3D[];$("input[name=3Did]:checked,input[name=3Dldda_ids]:checked").each(fun= ction(){var A=3D{data_type:"track_config",hda_ldda:"hda"},B=3D$(this).val()= ;if($(this).attr("name")!=3D=3D"id"){A.hda_ldda=3D"ldda"}z[z.length]=3D$.aj= ax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(= ){var A=3D(arguments[0] instanceof Array?$.map(arguments,function(B){return= B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=3Dfunction(u){retu= rn("isResolved" in u)};var f=3Dfunction(u){this.default_font=3Du!=3D=3Dunde= fined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=3Dthis.ne= w_canvas();this.dummy_context=3Dthis.dummy_canvas.getContext("2d");this.dum= my_context.font=3Dthis.default_font;this.char_width_px=3Dthis.dummy_context= .measureText("A").width;this.patterns=3D{};this.load_pattern("right_strand"= ,"/visualization/strand_right.png");this.load_pattern("left_strand","/visua= lization/strand_left.png");this.load_pattern("right_strand_inv","/visualiza= tion/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualiza= tion/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y= ){var v=3Dthis.patterns,w=3Dthis.dummy_context,x=3Dnew Image();x.src=3Dgala= xy_paths.attributes.image_path+y;x.onload=3Dfunction(){v[u]=3Dw.createPatte= rn(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canva= s:function(){var u=3D$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlC= anvasManager.initElement(u)}u.manager=3Dthis;return u}});var q=3DBackbone.M= odel.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initial= ize:function(u){this.clear()},get_elt:function(v){var w=3Dthis.attributes.o= bj_cache,x=3Dthis.attributes.key_ary,u=3Dx.indexOf(v);if(u!=3D=3D-1){if(w[v= ].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w= [v]},set_elt:function(v,x){var y=3Dthis.attributes.obj_cache,z=3Dthis.attri= butes.key_ary,w=3Dthis.attributes.num_elements;if(!y[v]){if(z.length>=3Dw){= var u=3Dz.shift();delete y[u]}z.push(v)}y[v]=3Dx;return x},move_key_to_end:= function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.p= ush(v)},clear:function(){this.attributes.obj_cache=3D{};this.attributes.key= _ary=3D[]},size:function(){return this.attributes.key_ary.length}});var d= =3Dq.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,init_d= ata:null,filters_manager:null,data_type:"data",data_mode_compatible:functio= n(u,v){return true},can_subset:function(u){return false}}),initialize:funct= ion(u){q.prototype.initialize.call(this);var v=3Dthis.get("init_data");if(v= ){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.len= gth){this.set("num_elements",u.length)}var v=3Dthis;s.each(u,function(w){v.= set_data(w.region,w)})},data_is_ready:function(){var x=3Dthis.get("dataset"= ),w=3D$.Deferred(),u=3D(this.get("data_type")=3D=3D"raw_data"?"state":this.= get("data_type")=3D=3D"data"?"converted_datasets_state":"error"),v=3Dnew l.= ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda= _ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success= _fn:function(y){return y!=3D=3D"pending"}});$.when(v.go()).then(function(y)= {w.resolve(y=3D=3D=3D"ok"||y=3D=3D=3D"data")});return w},search_features:fu= nction(u){var v=3Dthis.get("dataset"),w=3D{query:u,hda_ldda:v.get("hda_ldda= "),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,= B,v,A){var y=3Dthis.get("dataset"),x=3D{data_type:this.get("data_type"),chr= om:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,= hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=3Dthis.get("filters_manager= ");if(E){var F=3D[];var u=3DE.filters;for(var z=3D0;z<u.length;z++){F.push(= u[z].name)}x.filter_cols=3DJSON.stringify(F)}var w=3Dthis,D=3D$.getJSON(y.u= rl(),x,function(G){w.set_data(C,G)});this.set_data(C,D);return D},get_data:= function(A,z,w,y){var B=3Dthis.get_elt(A);if(B&&(j(B)||this.get("data_mode_= compatible")(B,z))){return B}var C=3Dthis.get("key_ary"),v=3Dthis.get("obj_= cache"),D,u;for(var x=3D0;x<C.length;x++){D=3DC[x];u=3Dnew g({from_str:D});= if(u.contains(A)){B=3Dv[D];if(j(B)||(this.get("data_mode_compatible")(B,z)&= &this.get("can_subset")(B))){this.move_key_to_end(D,x);return B}}}return th= is.load_data(A,z,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_= REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E= =3Dthis._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){cons= ole.log("ERROR: problem with getting more data: current data is not compati= ble");return}var w=3DC.get("start");if(y=3D=3D=3Dthis.DEEP_DATA_REQ){$.exte= nd(A,{start_val:E.data.length+1})}else{if(y=3D=3D=3Dthis.BROAD_DATA_REQ){w= =3D(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=3DC.copy().s= et("start",w);var v=3Dthis,z=3Dthis.load_data(D,B,x,A),u=3D$.Deferred();thi= s.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=3DE.data.conca= t(F.data);if(F.max_low){F.max_low=3DE.max_low}if(F.message){F.message=3DF.m= essage.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});retu= rn u},can_get_more_detailed_data:function(v){var u=3Dthis.get_elt(v);return= (u.dataset_type=3D=3D=3D"bigwig"&&u.data.length<8000)},get_more_detailed_da= ta:function(x,z,v,y,w){var u=3Dthis._mark_stale(x);if(!u){console.log("ERRO= R getting more detailed data: no current data");return}if(!w){w=3D{}}if(u.d= ataset_type=3D=3D=3D"bigwig"){w.num_samples=3D1000*y}else{if(u.dataset_type= =3D=3D=3D"summary_tree"){w.level=3DMath.min(u.level-1,2)}}return this.load_= data(x,z,v,w)},_mark_stale:function(v){var u=3Dthis.get_elt(v);if(!u){conso= le.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString()= )}u.stale=3Dtrue;return u},get_genome_wide_data:function(u){var w=3Dthis,y= =3Dtrue,x=3Ds.map(u.get("chroms_info").chrom_info,function(A){var z=3Dw.get= _elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=3Dfalse}return z});= if(y){return x}var v=3D$.Deferred();$.getJSON(this.get("dataset").url(),{da= ta_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});r= eturn v},get_elt:function(u){return q.prototype.get_elt.call(this,u.toStrin= g())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString= (),u)}});var n=3Dd.extend({initialize:function(u){var v=3Dnew Backbone.Mode= l();v.urlRoot=3Du.data_url;this.set("dataset",v)},load_data:function(w,x,u,= v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,w,x,u,v= )}});var c=3DBackbone.Model.extend({defaults:{name:null,key:null,chroms_inf= o:null},initialize:function(u){this.id=3Du.dbkey},get_chroms_info:function(= ){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(= u){var v=3Ds.find(this.get_chroms_info(),function(w){return w.chrom=3D=3Du}= );return new g({chrom:v.chrom,end:v.len})}});var g=3DBackbone.RelationalMod= el.extend({defaults:{chrom:null,start:0,end:0},initialize:function(v){if(v.= from_str){var x=3Dv.from_str.split(":"),w=3Dx[0],u=3Dx[1].split("-");this.s= et({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function= (){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.g= et("end")})},length:function(){return this.get("end")-this.get("start")},to= String:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.g= et("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get(= "start"),end:this.get("end")}},compute_overlap:function(B){var v=3Dthis.get= ("chrom"),A=3DB.get("chrom"),z=3Dthis.get("start"),x=3DB.get("start"),y=3Dt= his.get("end"),w=3DB.get("end"),u;if(v&&A&&v!=3D=3DA){return g.overlap_resu= lts.DIF_CHROMS}if(z<x){if(y<x){u=3Dg.overlap_results.BEFORE}else{if(y<=3Dw)= {u=3Dg.overlap_results.OVERLAP_START}else{u=3Dg.overlap_results.CONTAINS}}}= else{if(z>w){u=3Dg.overlap_results.AFTER}else{if(y<=3Dw){u=3Dg.overlap_resu= lts.CONTAINED_BY}else{u=3Dg.overlap_results.OVERLAP_END}}}return u},contain= s:function(u){return this.compute_overlap(u)=3D=3D=3Dg.overlap_results.CONT= AINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],= [g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AF= TER]).length=3D=3D=3D0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONT= AINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}= });var m=3DBackbone.Collection.extend({model:g});var e=3DBackbone.Relationa= lModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.Has= One,key:"region",relatedModel:g}]});var r=3DBackbone.Collection.extend({mod= el:e});var t=3Di.Dataset.extend({initialize:function(u){this.set("id",u.dat= aset_id);this.set("config",p.ConfigSettingCollection.from_config_dict(u.pre= fs));this.get("config").add([{key:"name",value:this.get("name")},{key:"colo= r"}]);var v=3Dthis.get("preloaded_data");if(v){v=3Dv.data}else{v=3D[]}this.= set("data_manager",new d({dataset:this,init_data:v}))}});var o=3DBackbone.R= elationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("vi= sualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST"= ,dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=3Do.extend= ({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks= :null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relate= dModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=3DBack= bone.Model.extend({});var h=3DBackbone.Router.extend({initialize:function(v= ){this.view=3Dv.view;this.route(/([\w]+)$/,"change_location");this.route(/(= [\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=3Dthis;u.view.on("navigate= ",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(= u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,= Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeR= egionCollection:m,GenomeVisualization:k,ReferenceTrackDataManager:n,TrackBr= owserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -10,7 +10,7 @@ "../libs/d3", =20 "../libs/bootstrap", - "../libs/jquery/jquery-ui-1.8.23.custom.min" + "../libs/jquery/jquery-ui" ], function(){ =20 /* =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/requests/select_datasets_to_transfer.mako --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -8,7 +8,7 @@ ${common_javascripts()} </%def> =20 -${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.coo= kie", "libs/jquery/jquery.dynatree" )} +${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jquery= /jquery.dynatree" )} ${h.css( "dynatree_skin/ui.dynatree" )} =20 <script type=3D"text/javascript"> diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/tool_shed_repository/browse_repository.ma= ko --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -9,7 +9,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.dynatree" )} ${browse_files(repository.name, repository.repo_files_directory(trans.= app))} </%def> =20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/tool_shed_repository/browse_tool_dependen= cy.mako --- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako +++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako @@ -9,7 +9,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.dynatree" )} ${browse_files(tool_dependency.name, tool_dependency.installation_dire= ctory( trans.app ))} </%def> =20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -23,8 +23,6 @@ <![endif]--> =20 ${render_trackster_js_files()} -${h.js( "libs/jquery/jquery.autocomplete" )} - =20 <script type=3D"text/javascript"> =20 @@ -107,7 +105,12 @@ "Create": function() { $(document).trigger("conver= t_to_values"); continue_fn(); } }); $("#new-title").focus(); - replace_big_select_inputs(); + $("select[name=3D'dbkey']").combobox({ + appendTo: $("#overlay"), + size: 40 + }); + // To support the large number of options for dbkey, e= nable scrolling in overlay. + $("#overlay").css("overflow", "auto"); } }); %endif diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -5,7 +5,7 @@ ${h.css( "base", "autocomplete_tagging", - "jquery-ui/smoothness/jquery-ui-1.8.23.custom" + "jquery-ui/smoothness/jquery-ui" )} =20 <style type=3D"text/css"> diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/sweepster.mako --- a/templates/visualization/sweepster.mako +++ b/templates/visualization/sweepster.mako @@ -107,7 +107,7 @@ ${parent.javascripts()} =20 ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form= " )} - ${h.js( "libs/require", "libs/jquery/jquery-ui-1.8.23.custom.min" )} + ${h.js( "libs/require", "libs/jquery/jquery-ui" )} =20 <script type=3D"text/javascript"> require.config({=20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -5,13 +5,14 @@ ## Render needed CSS files. <%def name=3D"render_trackster_css_files()"> ${h.css( "history", "autocomplete_tagging", "trackster", "library",=20 - "jquery-ui/smoothness/jquery-ui-1.8.23.custom" )} + "jquery-ui/smoothness/jquery-ui" )} </%def> =20 =20 ## Render needed JavaScript files. <%def name=3D"render_trackster_js_files()"> - ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.e= vent.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel= ", "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/require", "libs/farbtas= tic" )} + ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.e= vent.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel= ", "libs/jquery/jquery-ui", "libs/jquery/jquery-ui-combobox", + "libs/require", "libs/farbtastic" )} </%def> =20 ## Render a block of JavaScript that contains all necessary variables for = Trackster. diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/webapps/community/repository/browse_repository.= mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -58,7 +58,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui-1.8.23.cus= tom.min", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui", "libs/jq= uery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${common_javascripts(repository)} </%def> =20 diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -28,7 +28,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jq= uery/jquery.dynatree" )} ${common_javascripts(repository)} <script type=3D"text/javascript"> $( function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: GFF/GTF reading and visualization enhancements: (a) enable GFF to FLI conversion and (b) better feature aggregation.
by Bitbucket 29 Oct '12

29 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fa045aad74e9/ changeset: fa045aad74e9 user: jgoecks date: 2012-10-29 15:44:32 summary: GFF/GTF reading and visualization enhancements: (a) enable GFF to FLI conversion and (b) better feature aggregation. affected #: 4 files diff -r ecd131b136d00d5753992061d12b12156be8b277 -r fa045aad74e90f16995e0cbb670a59e6b9becbed lib/galaxy/datatypes/converters/bed_to_fli_converter.xml --- a/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml @@ -1,7 +1,7 @@ <tool id="CONVERTER_bed_to_fli_0" name="Convert BED to Feature Location Index"> - <command interpreter="python">interval_to_fli.py -B $input1 $output1</command> + <command interpreter="python">interval_to_fli.py -F bed $input1 $output1</command><inputs><param format="bed" name="input1" type="data" label="Choose BED file"/></inputs> diff -r ecd131b136d00d5753992061d12b12156be8b277 -r fa045aad74e90f16995e0cbb670a59e6b9becbed lib/galaxy/datatypes/converters/gff_to_fli_converter.xml --- a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml +++ b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml @@ -1,7 +1,7 @@ <tool id="CONVERTER_gff_to_fli_0" name="Convert GFF to Feature Location Index"> - <command interpreter="python">interval_to_fli.py -G $input1 $output1</command> + <command interpreter="python">interval_to_fli.py -F $input1.extension $input1 $output1</command><inputs><param format="gff" name="input1" type="data" label="Choose GFF file"/></inputs> diff -r ecd131b136d00d5753992061d12b12156be8b277 -r fa045aad74e90f16995e0cbb670a59e6b9becbed lib/galaxy/datatypes/converters/interval_to_fli.py --- a/lib/galaxy/datatypes/converters/interval_to_fli.py +++ b/lib/galaxy/datatypes/converters/interval_to_fli.py @@ -12,22 +12,28 @@ import sys, optparse from galaxy import eggs -from galaxy.datatypes.util.gff_util import read_unordered_gtf, convert_gff_coords_to_bed +from galaxy.datatypes.util.gff_util import GFFReaderWrapper, read_unordered_gtf, convert_gff_coords_to_bed def main(): # Process arguments. parser = optparse.OptionParser() - parser.add_option( '-B', '--bed', action="store_true", dest="bed_input" ) - parser.add_option( '-G', '--gff', action="store_true", dest="gff_input" ) + parser.add_option( '-F', '--format', dest="input_format" ) (options, args) = parser.parse_args() in_fname, out_fname = args - + input_format = options.input_format.lower() # Create dict of name-location pairings. name_loc_dict = {} - if options.gff_input: - # GFF format - for feature in read_unordered_gtf( open( in_fname, 'r' ) ): + if input_format in [ 'gff', 'gtf' ]: + # GTF/GFF format + + # Create reader. + if input_format == 'gff': + in_reader = GFFReaderWrapper( open( in_fname, 'r' ) ) + else: #input_format == 'gtf' + in_reader = read_unordered_gtf( open( in_fname, 'r' ) ) + + for feature in in_reader: for name in feature.attributes: val = feature.attributes[ name ] try: @@ -50,7 +56,7 @@ loc[ 'start' ] = feature.start if feature.end > loc[ 'end' ]: loc[ 'end' ] = feature.end - else: + elif input_format == 'bed': # BED format. for line in open( in_fname, 'r' ): # Ignore track lines. diff -r ecd131b136d00d5753992061d12b12156be8b277 -r fa045aad74e90f16995e0cbb670a59e6b9becbed lib/galaxy/datatypes/util/gff_util.py --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -227,22 +227,20 @@ continue # Determine if interval is part of feature. - part_of = True + part_of = False group = interval.attributes.get( 'group', None ) # GFF test: - if group and feature_group != group: - part_of = False + if group and feature_group == group: + part_of = True # GFF3 test: parent_id = interval.attributes.get( 'Parent', None ) cur_id = interval.attributes.get( 'ID', None ) - if ( cur_id and cur_id != feature_id ) or ( parent_id and parent_id != feature_id ): - part_of = False + if ( cur_id and cur_id == feature_id ) or ( parent_id and parent_id == feature_id ): + part_of = True # GTF test: - gene_id = interval.attributes.get( 'gene_id', None ) transcript_id = interval.attributes.get( 'transcript_id', None ) - if ( transcript_id and transcript_id != feature_transcript_id ) or \ - ( gene_id and gene_id != feature_gene_id ): - part_of = False + if transcript_id and transcript_id == feature_transcript_id: + part_of = True # If interval is not part of feature, clean up and break. if not part_of: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: libraries: fix in query for 'datasets_are_public'
by Bitbucket 26 Oct '12

26 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ecd131b136d0/ changeset: ecd131b136d0 user: james_taylor date: 2012-10-26 22:23:01 summary: libraries: fix in query for 'datasets_are_public' affected #: 1 file diff -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a -r ecd131b136d00d5753992061d12b12156be8b277 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -879,7 +879,7 @@ # Now get all datasets which have DATASET_ACCESS actions: access_data_perms = trans.sa_session.query( trans.app.model.DatasetPermissions ) \ - .filter( and_( trans.app.model.DatasetPermissions.dataset_id in dataset_ids, + .filter( and_( trans.app.model.DatasetPermissions.dataset_id.in_( dataset_ids ), trans.app.model.DatasetPermissions.action == self.permitted_actions.DATASET_ACCESS.action ) ) \ .all() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Refactor code supporting setting metadata on repositories in the tool shed and installed in Galaxy - enables using same code across web apps.
by Bitbucket 26 Oct '12

26 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/50b1d7a65bd2/ changeset: 50b1d7a65bd2 user: greg date: 2012-10-26 21:39:50 summary: Refactor code supporting setting metadata on repositories in the tool shed and installed in Galaxy - enables using same code across web apps. affected #: 14 files diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -3,9 +3,12 @@ from datetime import date, datetime, timedelta from time import strftime, gmtime from galaxy import util +from galaxy.web import url_for +from galaxy.web.form_builder import SelectField from galaxy.tools import parameters from galaxy.datatypes.checkers import * from galaxy.util.json import * +from galaxy.util import inflector from galaxy.tools.search import ToolBoxSearch from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment from galaxy.tool_shed.encoding_util import * @@ -23,6 +26,7 @@ log = logging.getLogger( __name__ ) +GALAXY_ADMIN_TOOL_SHED_CONTROLLER = 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER' INITIAL_CHANGELOG_HASH = '000000000000' # Characters that must be html escaped MAPPED_CHARS = { '>' :'>', @@ -33,6 +37,7 @@ MAX_CONTENT_SIZE = 32768 NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'tool_dependencies.xml' ] VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) +TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER' class ShedCounter( object ): def __init__( self, model ): @@ -246,6 +251,27 @@ except: pass return converter_path, display_path +def build_repository_ids_select_field( trans, cntrller, name='repository_ids', multiple=True, display='checkboxes' ): + """Method called from both Galaxy and the Tool Shed to generate the current list of repositories for resetting metadata.""" + repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) + if cntrller == TOOL_SHED_ADMIN_CONTROLLER: + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ) \ + .order_by( trans.model.Repository.table.c.name, + trans.model.Repository.table.c.user_id ): + owner = repository.user.username + option_label = '%s (%s)' % ( repository.name, owner ) + option_value = '%s' % trans.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + elif cntrller == GALAXY_ADMIN_TOOL_SHED_CONTROLLER: + for repository in trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( trans.model.ToolShedRepository.table.c.uninstalled == False ) \ + .order_by( trans.model.ToolShedRepository.table.c.name, + trans.model.ToolShedRepository.table.c.owner ): + option_label = '%s (%s)' % ( repository.name, repository.owner ) + option_value = trans.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return repositories_select_field def can_generate_tool_dependency_metadata( root, metadata_dict ): """ Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml @@ -339,6 +365,105 @@ correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) return invalid_files_and_errors_tups +def clean_repository_metadata( trans, id, changeset_revisions ): + # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions. + # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older + # records, so we'll order by update_time descending and delete records that have the same changeset_revision we come across later.. + changeset_revisions_checked = [] + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ + .order_by( trans.model.RepositoryMetadata.table.c.changeset_revision, + trans.model.RepositoryMetadata.table.c.update_time.desc() ): + changeset_revision = repository_metadata.changeset_revision + can_delete = changeset_revision in changeset_revisions_checked or changeset_revision not in changeset_revisions + if can_delete: + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() +def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): + # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of + # current_changeset_revision which is associated with current_metadata_dict. A new repository_metadata record will be created only + # when this method returns the string 'not equal and not subset'. + ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) + ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) + ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ] + ancestor_guids.sort() + ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', [] ) + ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) + current_datatypes = current_metadata_dict.get( 'datatypes', [] ) + current_tools = current_metadata_dict.get( 'tools', [] ) + current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] + current_guids.sort() + current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', [] ) + current_workflows = current_metadata_dict.get( 'workflows', [] ) + # Handle case where no metadata exists for either changeset. + if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes: + return 'no metadata' + workflow_comparison = compare_workflows( ancestor_workflows, current_workflows ) + datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) + # Handle case where all metadata is the same. + if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': + return 'equal' + if workflow_comparison in [ 'equal', 'subset' ] and datatype_comparison in [ 'equal', 'subset' ]: + is_subset = True + for guid in ancestor_guids: + if guid not in current_guids: + is_subset = False + break + if is_subset: + return 'subset' + return 'not equal and not subset' +def compare_datatypes( ancestor_datatypes, current_datatypes ): + # Determine if ancestor_datatypes is the same as current_datatypes + # or if ancestor_datatypes is a subset of current_datatypes. Each + # datatype dict looks something like: + # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} + if len( ancestor_datatypes ) <= len( current_datatypes ): + for ancestor_datatype in ancestor_datatypes: + # Currently the only way to differentiate datatypes is by name. + ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ] + ancestor_datatype_extension = ancestor_datatype[ 'extension' ] + ancestor_datatype_mimetype = ancestor_datatype.get( 'mimetype', None ) + found_in_current = False + for current_datatype in current_datatypes: + if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \ + current_datatype[ 'extension' ] == ancestor_datatype_extension and \ + current_datatype.get( 'mimetype', None ) == ancestor_datatype_mimetype: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_datatypes ) == len( current_datatypes ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' +def compare_workflows( ancestor_workflows, current_workflows ): + # Determine if ancestor_workflows is the same as current_workflows + # or if ancestor_workflows is a subset of current_workflows. + if len( ancestor_workflows ) <= len( current_workflows ): + for ancestor_workflow_tup in ancestor_workflows: + # ancestor_workflows is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + ancestor_workflow_dict = ancestor_workflow_tup[1] + # Currently the only way to differentiate workflows is by name. + ancestor_workflow_name = ancestor_workflow_dict[ 'name' ] + num_ancestor_workflow_steps = len( ancestor_workflow_dict[ 'steps' ] ) + found_in_current = False + for current_workflow_tup in current_workflows: + current_workflow_dict = current_workflow_tup[1] + # Assume that if the name and number of steps are euqal, + # then the workflows are the same. Of course, this may + # not be true... + if current_workflow_dict[ 'name' ] == ancestor_workflow_name and len( current_workflow_dict[ 'steps' ] ) == num_ancestor_workflow_steps: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_workflows ) == len( current_workflows ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' def concat_messages( msg1, msg2 ): if msg1: if msg2: @@ -447,6 +572,20 @@ tool_dicts=tool_dicts, converter_path=converter_path, display_path=display_path ) +def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): + downloadable = is_downloadable( metadata_dict ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + repository_metadata.metadata = metadata_dict + repository_metadata.downloadable = downloadable + else: + repository_metadata = trans.model.RepositoryMetadata( repository_id=repository.id, + changeset_revision=changeset_revision, + metadata=metadata_dict, + downloadable=downloadable ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + return repository_metadata def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ): # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used @@ -546,10 +685,19 @@ set_status=set_status ) tool_dependency_objects.append( tool_dependency ) return tool_dependency_objects -def generate_clone_url( trans, repository ): - """Generate the URL for cloning a repository.""" +def generate_clone_url_for_installed_repository( trans, repository ): + """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) return url_join( tool_shed_url, 'repos', repository.owner, repository.name ) +def generate_clone_url_for_repository_in_tool_shed( trans, repository ): + """Generate the URL for cloning a repository that is in the tool shed.""" + base_url = url_for( '/', qualified=True ).rstrip( '/' ) + if trans.user: + protocol, base = base_url.split( '://' ) + username = '%s@' % trans.user.username + return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) + else: + return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) def generate_datatypes_metadata( datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree = ElementTree.parse( datatypes_config ) @@ -750,6 +898,42 @@ app.config.tool_data_path = original_tool_data_path app.config.tool_data_table_config_path = original_tool_data_table_config_path return metadata_dict, invalid_file_tups +def generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False ): + if as_html: + new_line = '<br/>' + bold_start = '<b>' + bold_end = '</b>' + else: + new_line = '\n' + bold_start = '' + bold_end = '' + message = '' + if not displaying_invalid_tool: + if metadata_dict: + message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) + message += "Correct the following problems if necessary and reset metadata.%s" % new_line + else: + message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) + message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.%s" % new_line + for itc_tup in invalid_file_tups: + tool_file, exception_msg = itc_tup + if exception_msg.find( 'No such file or directory' ) >= 0: + exception_items = exception_msg.split() + missing_file_items = exception_items[ 7 ].split( '/' ) + missing_file = missing_file_items[ -1 ].rstrip( '\'' ) + if missing_file.endswith( '.loc' ): + sample_ext = '%s.sample' % missing_file + else: + sample_ext = missing_file + correction_msg = "This file refers to a missing file %s%s%s. " % ( bold_start, str( missing_file ), bold_end ) + correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % ( bold_start, sample_ext, bold_end ) + else: + if as_html: + correction_msg = exception_msg + else: + correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end ) + message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) + return message def generate_package_dependency_metadata( elem, tool_dependencies_dict ): """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set.""" requirements_dict = {} @@ -1158,6 +1342,9 @@ ctx = get_changectx_for_changeset( repo, changeset_revision ) named_tmp_file = get_named_tmpfile_from_ctx( ctx, file_name, dir ) return named_tmp_file +def get_installed_tool_shed_repository( trans, id ): + """Get a repository on the Galaxy side from the database via id""" + return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) def get_list_of_copied_sample_files( repo, ctx, dir ): """ Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy @@ -1211,6 +1398,24 @@ fh.close() return tmp_filename return None +def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): + parent_id = None + # Compare from most recent to oldest. + changeset_revisions.reverse() + for changeset_revision in changeset_revisions: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + metadata = repository_metadata.metadata + tools_dicts = metadata.get( 'tools', [] ) + for tool_dict in tools_dicts: + if tool_dict[ 'guid' ] == guid: + # The tool has not changed between the compared changeset revisions. + continue + if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version: + # The tool version is different, so we've found the parent. + return tool_dict[ 'guid' ] + if parent_id is None: + # The tool did not change through all of the changeset revisions. + return old_id def get_repository_file_contents( file_path ): if is_gzip( file_path ): to_html = to_html_str( '\ngzip compressed file\n' ) @@ -1242,6 +1447,9 @@ if contents: contents.sort() return contents +def get_repository_in_tool_shed( trans, id ): + """Get a repository on the tool shed side from the database via id""" + return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database""" # Make sure there are no duplicate records, and return the single unique record for the changeset_revision. Duplicate records were somehow @@ -1635,6 +1843,8 @@ parent_id=tool_version_using_parent_id.id ) sa_session.add( tool_version_association ) sa_session.flush() +def is_downloadable( metadata_dict ): + return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ): # Load or deactivate proprietary datatype converters app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=installed_repository_dict, deactivate=deactivate ) @@ -1739,6 +1949,12 @@ repo, source=repository_clone_url, rev=[ ctx_rev ] ) +def remove_dir( dir ): + if os.path.exists( dir ): + try: + shutil.rmtree( dir ) + except: + pass def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ): # A tool shed repository is being uninstalled so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have @@ -1912,6 +2128,188 @@ removed = True error_message = '' return removed, error_message +def reset_all_metadata_on_installed_repository( trans, id ): + """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" + repository = get_installed_tool_shed_repository( trans, id ) + tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) + repository_clone_url = generate_clone_url_for_installed_repository( trans, repository ) + tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) + if relative_install_dir: + original_metadata_dict = repository.metadata + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False ) + repository.metadata = metadata_dict + if metadata_dict != original_metadata_dict: + update_in_shed_tool_config( trans.app, repository ) + trans.sa_session.add( repository ) + trans.sa_session.flush() + log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + else: + log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + else: + log.debug( 'Error locating installation directory for repository %s.' % repository.name ) + return invalid_file_tups, metadata_dict +def reset_all_metadata_on_repository_in_tool_shed( trans, id ): + """Reset all metadata on a single repository in a tool shed.""" + def reset_all_tool_versions( trans, id, repo ): + changeset_revisions = [] + for changeset in repo.changelog: + changeset_revision = str( repo.changectx( changeset ) ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if metadata.get( 'tools', None ): + changeset_revisions.append( changeset_revision ) + # The list of changeset_revisions is now filtered to contain only those that are downloadable and contain tools. + # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. + for index, changeset_revision in enumerate( changeset_revisions ): + tool_versions_dict = {} + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + metadata = repository_metadata.metadata + tool_dicts = metadata[ 'tools' ] + if index == 0: + # The first changset_revision is a special case because it will have no ancestor changeset_revisions in which to match tools. + # The parent tool id for tools in the first changeset_revision will be the "old_id" in the tool config. + for tool_dict in tool_dicts: + tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] + else: + for tool_dict in tool_dicts: + parent_id = get_parent_id( trans, + id, + tool_dict[ 'id' ], + tool_dict[ 'version' ], + tool_dict[ 'guid' ], + changeset_revisions[ 0:index ] ) + tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id + if tool_versions_dict: + repository_metadata.tool_versions = tool_versions_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + repository = get_repository_in_tool_shed( trans, id ) + log.debug( "Resetting all metadata on repository: %s" % repository.name ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository ) + # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop + # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. + changeset_revisions = [] + # When a new repository_metadata record is created, it always uses the values of metadata_changeset_revision and metadata_dict. + metadata_changeset_revision = None + metadata_dict = None + ancestor_changeset_revision = None + ancestor_metadata_dict = None + invalid_file_tups = [] + home_dir = os.getcwd() + for changeset in repo.changelog: + work_dir = tempfile.mkdtemp() + current_changeset_revision = str( repo.changectx( changeset ) ) + ctx = repo.changectx( changeset ) + log.debug( "Cloning repository revision: %s", str( ctx.rev() ) ) + cloned_ok, error_message = clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + if cloned_ok: + log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) + current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + repository_clone_url=repository_clone_url, + relative_install_dir=repo_dir, + repository_files_dir=work_dir, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False ) + if current_metadata_dict: + if not metadata_changeset_revision and not metadata_dict: + # We're at the first change set in the change log. + metadata_changeset_revision = current_changeset_revision + metadata_dict = current_metadata_dict + if ancestor_changeset_revision: + # Compare metadata from ancestor and current. The value of comparison will be one of: + # 'no metadata' - no metadata for either ancestor or current, so continue from current + # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current + # 'subset' - ancestor metadata is a subset of current metadata, so continue from current + # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. + comparison = compare_changeset_revisions( ancestor_changeset_revision, + ancestor_metadata_dict, + current_changeset_revision, + current_metadata_dict ) + if comparison in [ 'no metadata', 'equal', 'subset' ]: + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + elif comparison == 'not equal and not subset': + metadata_changeset_revision = ancestor_changeset_revision + metadata_dict = ancestor_metadata_dict + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + else: + # We're at the beginning of the change log. + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + if not ctx.children(): + metadata_changeset_revision = current_changeset_revision + metadata_dict = current_metadata_dict + # We're at the end of the change log. + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + elif ancestor_metadata_dict: + # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + if not ctx.children(): + # We're at the end of the change log. + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + remove_dir( work_dir ) + # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. + clean_repository_metadata( trans, id, changeset_revisions ) + # Set tool version information for all downloadable changeset revisions. Get the list of changeset revisions from the changelog. + reset_all_tool_versions( trans, id, repo ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) + return invalid_file_tups, metadata_dict +def reset_metadata_on_selected_repositories( trans, **kwd ): + # This method is called from both Galaxy and the Tool Shed, so the cntrller param is required. + repository_ids = util.listify( kwd.get( 'repository_ids', None ) ) + CONTROLLER = kwd[ 'CONTROLLER' ] + message = '' + status = 'done' + if repository_ids: + successful_count = 0 + unsuccessful_count = 0 + for repository_id in repository_ids: + try: + if CONTROLLER == 'TOOL_SHED_ADMIN_CONTROLLER': + repository = get_repository_in_tool_shed( trans, repository_id ) + invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, repository_id ) + elif CONTROLLER == 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER': + repository = get_installed_tool_shed_repository( trans, repository_id ) + invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id ) + if invalid_file_tups: + message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False ) + log.debug( message ) + unsuccessful_count += 1 + else: + log.debug( "Successfully reset metadata on repository %s" % repository.name ) + successful_count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) + unsuccessful_count += 1 + message = "Successfully reset metadata on %d %s. " % ( successful_count, inflector.cond_plural( successful_count, "repository" ) ) + if unsuccessful_count: + message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count, + inflector.cond_plural( unsuccessful_count, "repository" ) ) + else: + message = 'Select at least one repository to on which to reset all metadata.' + status = 'error' + return message, status def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. app.tool_data_tables.data_tables = {} @@ -2061,7 +2459,7 @@ tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) - cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url( trans, repository ) ) + cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url_for_installed_repository( trans, repository ) ) tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) owner = repository.owner if not owner: diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -5,7 +5,9 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.web.form_builder import SelectField from galaxy.util import inflector -from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui +# TODO: re-factor shed_util to eliminate the following restricted imports +from galaxy.util.shed_util import build_repository_ids_select_field, get_changectx_for_changeset, get_configured_ui, get_repository_in_tool_shed +from galaxy.util.shed_util import reset_metadata_on_selected_repositories, TOOL_SHED_ADMIN_CONTROLLER from common import * from repository import RepositoryGrid, CategoryGrid @@ -481,7 +483,7 @@ # The received id is the repository id, so we need to get the id of the user # that uploaded the repository. repository_id = kwd.get( 'id', None ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) kwd[ 'f-email' ] = repository.user.email elif operation == "repositories_by_category": # Eliminate the current filters if any exist. @@ -513,7 +515,7 @@ changset_revision_str = 'changeset_revision_' if k.startswith( changset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -586,7 +588,7 @@ count = 0 deleted_repositories = "" for repository_id in ids: - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) if not repository.deleted: repository.deleted = True trans.sa_session.add( repository ) @@ -715,57 +717,14 @@ status=status ) @web.expose @web.require_admin - def reset_metadata_on_selected_repositories( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository_names_by_owner = util.listify( kwd.get( 'repository_names_by_owner', None ) ) + def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: - if repository_names_by_owner: - successful_count = 0 - unsuccessful_count = 0 - for repository_name_owner_str in repository_names_by_owner: - repository_name_owner_list = repository_name_owner_str.split( STRSEP ) - name = repository_name_owner_list[ 0 ] - owner = repository_name_owner_list[ 1 ] - repository = get_repository_by_name_and_owner( trans, name, owner ) - try: - invalid_file_tups, metadata_dict = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) - if invalid_file_tups: - message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False ) - log.debug( message ) - unsuccessful_count += 1 - else: - log.debug( "Successfully reset metadata on repository %s" % repository.name ) - successful_count += 1 - except Exception, e: - log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) - unsuccessful_count += 1 - message = "Successfully reset metadata on %d %s. " % ( successful_count, - inflector.cond_plural( successful_count, "repository" ) ) - if unsuccessful_count: - message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count, - inflector.cond_plural( unsuccessful_count, - "repository" ) ) - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repository_metadata', - message=util.sanitize_text( message ), - status=status ) ) - else: - 'Select at least one repository to on which to reset all metadata.' - status = 'error' - repositories_select_field = SelectField( name='repository_names_by_owner', - multiple=True, - display='checkboxes' ) - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ) \ - .order_by( trans.model.Repository.table.c.name, - trans.model.Repository.table.c.user_id ): - owner = repository.user.username - option_label = '%s (%s)' % ( repository.name, owner ) - option_value = '%s%s%s' % ( repository.name, STRSEP, owner ) - repositories_select_field.add_option( option_label, option_value ) + kwd[ 'CONTROLLER' ] = TOOL_SHED_ADMIN_CONTROLLER + message, status = reset_metadata_on_selected_repositories( trans, **kwd ) + else: + message = util.restore_text( kwd.get( 'message', '' ) ) + status = kwd.get( 'status', 'done' ) + repositories_select_field = build_repository_ids_select_field( trans, TOOL_SHED_ADMIN_CONTROLLER ) return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, @@ -783,7 +742,7 @@ count = 0 undeleted_repositories = "" for repository_id in ids: - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) if repository.deleted: repository.deleted = False trans.sa_session.add( repository ) diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -5,11 +5,14 @@ from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * -from galaxy.util.shed_util import check_tool_input_params, clone_repository, concat_messages, copy_sample_file, generate_metadata_for_changeset_revision +# TODO: re-factor shed_util to eliminate the following restricted imports +from galaxy.util.shed_util import check_tool_input_params, clone_repository, concat_messages, copy_sample_file, create_or_update_repository_metadata +from galaxy.util.shed_util import generate_clone_url_for_repository_in_tool_shed, generate_message_for_invalid_tools, generate_metadata_for_changeset_revision from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_file_context_from_ctx, get_named_tmpfile_from_ctx -from galaxy.util.shed_util import get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk -from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH -from galaxy.util.shed_util import load_tool_from_config, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import get_parent_id, get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, is_downloadable, load_tool_from_config, remove_dir +from galaxy.util.shed_util import reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * from galaxy.web.base.controllers.admin import * from galaxy.webapps.community import model @@ -171,105 +174,6 @@ if user_email in admin_users: return True return False -def clean_repository_metadata( trans, id, changeset_revisions ): - # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions. - # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older - # records, so we'll order by update_time descending and delete records that have the same changeset_revision we come across later.. - changeset_revisions_checked = [] - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ - .order_by( trans.model.RepositoryMetadata.table.c.changeset_revision, - trans.model.RepositoryMetadata.table.c.update_time.desc() ): - changeset_revision = repository_metadata.changeset_revision - can_delete = changeset_revision in changeset_revisions_checked or changeset_revision not in changeset_revisions - if can_delete: - trans.sa_session.delete( repository_metadata ) - trans.sa_session.flush() -def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): - # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of - # current_changeset_revision which is associated with current_metadata_dict. A new repository_metadata record will be created only - # when this method returns the string 'not equal and not subset'. - ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) - ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) - ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ] - ancestor_guids.sort() - ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', [] ) - ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) - current_datatypes = current_metadata_dict.get( 'datatypes', [] ) - current_tools = current_metadata_dict.get( 'tools', [] ) - current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] - current_guids.sort() - current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', [] ) - current_workflows = current_metadata_dict.get( 'workflows', [] ) - # Handle case where no metadata exists for either changeset. - if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes: - return 'no metadata' - workflow_comparison = compare_workflows( ancestor_workflows, current_workflows ) - datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) - # Handle case where all metadata is the same. - if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': - return 'equal' - if workflow_comparison in [ 'equal', 'subset' ] and datatype_comparison in [ 'equal', 'subset' ]: - is_subset = True - for guid in ancestor_guids: - if guid not in current_guids: - is_subset = False - break - if is_subset: - return 'subset' - return 'not equal and not subset' -def compare_datatypes( ancestor_datatypes, current_datatypes ): - # Determine if ancestor_datatypes is the same as current_datatypes - # or if ancestor_datatypes is a subset of current_datatypes. Each - # datatype dict looks something like: - # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} - if len( ancestor_datatypes ) <= len( current_datatypes ): - for ancestor_datatype in ancestor_datatypes: - # Currently the only way to differentiate datatypes is by name. - ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ] - ancestor_datatype_extension = ancestor_datatype[ 'extension' ] - ancestor_datatype_mimetype = ancestor_datatype.get( 'mimetype', None ) - found_in_current = False - for current_datatype in current_datatypes: - if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \ - current_datatype[ 'extension' ] == ancestor_datatype_extension and \ - current_datatype.get( 'mimetype', None ) == ancestor_datatype_mimetype: - found_in_current = True - break - if not found_in_current: - return 'not equal and not subset' - if len( ancestor_datatypes ) == len( current_datatypes ): - return 'equal' - else: - return 'subset' - return 'not equal and not subset' -def compare_workflows( ancestor_workflows, current_workflows ): - # Determine if ancestor_workflows is the same as current_workflows - # or if ancestor_workflows is a subset of current_workflows. - if len( ancestor_workflows ) <= len( current_workflows ): - for ancestor_workflow_tup in ancestor_workflows: - # ancestor_workflows is a list of tuples where each contained tuple is - # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - ancestor_workflow_dict = ancestor_workflow_tup[1] - # Currently the only way to differentiate workflows is by name. - ancestor_workflow_name = ancestor_workflow_dict[ 'name' ] - num_ancestor_workflow_steps = len( ancestor_workflow_dict[ 'steps' ] ) - found_in_current = False - for current_workflow_tup in current_workflows: - current_workflow_dict = current_workflow_tup[1] - # Assume that if the name and number of steps are euqal, - # then the workflows are the same. Of course, this may - # not be true... - if current_workflow_dict[ 'name' ] == ancestor_workflow_name and len( current_workflow_dict[ 'steps' ] ) == num_ancestor_workflow_steps: - found_in_current = True - break - if not found_in_current: - return 'not equal and not subset' - if len( ancestor_workflows ) == len( current_workflows ): - return 'equal' - else: - return 'subset' - return 'not equal and not subset' def copy_file_from_disk( filename, repo_dir, dir ): file_path = None found = False @@ -300,66 +204,6 @@ fh.close() return file_path return None -def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): - downloadable = is_downloadable( metadata_dict ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - if repository_metadata: - repository_metadata.metadata = metadata_dict - repository_metadata.downloadable = downloadable - else: - repository_metadata = trans.model.RepositoryMetadata( repository_id=repository.id, - changeset_revision=changeset_revision, - metadata=metadata_dict, - downloadable=downloadable ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - return repository_metadata -def generate_clone_url( trans, repository_id ): - """Generate the URL for cloning a repository.""" - repository = get_repository( trans, repository_id ) - base_url = url_for( '/', qualified=True ).rstrip( '/' ) - if trans.user: - protocol, base = base_url.split( '://' ) - username = '%s@' % trans.user.username - return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) - else: - return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) -def generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False ): - if as_html: - new_line = '<br/>' - bold_start = '<b>' - bold_end = '</b>' - else: - new_line = '\n' - bold_start = '' - bold_end = '' - message = '' - if not displaying_invalid_tool: - if metadata_dict: - message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) - message += "Correct the following problems if necessary and reset metadata.%s" % new_line - else: - message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) - message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.%s" % new_line - for itc_tup in invalid_file_tups: - tool_file, exception_msg = itc_tup - if exception_msg.find( 'No such file or directory' ) >= 0: - exception_items = exception_msg.split() - missing_file_items = exception_items[ 7 ].split( '/' ) - missing_file = missing_file_items[ -1 ].rstrip( '\'' ) - if missing_file.endswith( '.loc' ): - sample_ext = '%s.sample' % missing_file - else: - sample_ext = missing_file - correction_msg = "This file refers to a missing file %s%s%s. " % ( bold_start, str( missing_file ), bold_end ) - correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % ( bold_start, sample_ext, bold_end ) - else: - if as_html: - correction_msg = exception_msg - else: - correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end ) - message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) - return message def generate_tool_guid( trans, repository, tool ): """ Generate a guid for the received tool. The form of the guid is @@ -450,24 +294,6 @@ fh.close() return tmp_filename return None -def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): - parent_id = None - # Compare from most recent to oldest. - changeset_revisions.reverse() - for changeset_revision in changeset_revisions: - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - metadata = repository_metadata.metadata - tools_dicts = metadata.get( 'tools', [] ) - for tool_dict in tools_dicts: - if tool_dict[ 'guid' ] == guid: - # The tool has not changed between the compared changeset revisions. - continue - if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version: - # The tool version is different, so we've found the parent. - return tool_dict[ 'guid' ] - if parent_id is None: - # The tool did not change through all of the changeset revisions. - return old_id def get_previous_downloadable_changset_revision( repository, repo, before_changeset_revision ): """ Return the downloadable changeset_revision in the repository changelog just prior to the changeset to which before_changeset_revision @@ -542,9 +368,6 @@ for changeset in repo.changelog: reversed_changelog.insert( 0, changeset ) return reversed_changelog -def get_repository( trans, id ): - """Get a repository from the database via id""" - return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() @@ -707,8 +530,6 @@ if previous_changeset_revision in reviewed_revision_hashes: return True return False -def is_downloadable( metadata_dict ): - return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): """ Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision @@ -716,7 +537,7 @@ revision and the first changeset revision in the repository, searching backwards. """ original_tool_data_path = trans.app.config.tool_data_path - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) message = '' @@ -802,134 +623,6 @@ return True # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed. return False -def remove_dir( dir ): - if os.path.exists( dir ): - try: - shutil.rmtree( dir ) - except: - pass -def reset_all_metadata_on_repository( trans, id, **kwd ): - def reset_all_tool_versions( trans, id, repo ): - changeset_revisions = [] - for changeset in repo.changelog: - changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if metadata.get( 'tools', None ): - changeset_revisions.append( changeset_revision ) - # The list of changeset_revisions is now filtered to contain only those that are downloadable and contain tools. - # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. - for index, changeset_revision in enumerate( changeset_revisions ): - tool_versions_dict = {} - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - metadata = repository_metadata.metadata - tool_dicts = metadata[ 'tools' ] - if index == 0: - # The first changset_revision is a special case because it will have no ancestor changeset_revisions in which to match tools. - # The parent tool id for tools in the first changeset_revision will be the "old_id" in the tool config. - for tool_dict in tool_dicts: - tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] - else: - for tool_dict in tool_dicts: - parent_id = get_parent_id( trans, - id, - tool_dict[ 'id' ], - tool_dict[ 'version' ], - tool_dict[ 'guid' ], - changeset_revisions[ 0:index ] ) - tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id - if tool_versions_dict: - repository_metadata.tool_versions = tool_versions_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) - log.debug( "Resetting all metadata on repository: %s" % repository.name ) - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - repository_clone_url = generate_clone_url( trans, id ) - # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop - # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. - changeset_revisions = [] - # When a new repository_metadata record is created, it always uses the values of metadata_changeset_revision and metadata_dict. - metadata_changeset_revision = None - metadata_dict = None - ancestor_changeset_revision = None - ancestor_metadata_dict = None - invalid_file_tups = [] - home_dir = os.getcwd() - for changeset in repo.changelog: - work_dir = tempfile.mkdtemp() - current_changeset_revision = str( repo.changectx( changeset ) ) - ctx = repo.changectx( changeset ) - log.debug( "Cloning repository revision: %s", str( ctx.rev() ) ) - cloned_ok, error_message = clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) - if cloned_ok: - log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - updating_installed_repository=False ) - if current_metadata_dict: - if not metadata_changeset_revision and not metadata_dict: - # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict - if ancestor_changeset_revision: - # Compare metadata from ancestor and current. The value of comparison will be one of: - # 'no metadata' - no metadata for either ancestor or current, so continue from current - # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current - # 'subset' - ancestor metadata is a subset of current metadata, so continue from current - # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. - comparison = compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) - if comparison in [ 'no metadata', 'equal', 'subset' ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - elif comparison == 'not equal and not subset': - metadata_changeset_revision = ancestor_changeset_revision - metadata_dict = ancestor_metadata_dict - repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - else: - # We're at the beginning of the change log. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict - # We're at the end of the change log. - repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. - if not ctx.children(): - # We're at the end of the change log. - repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - remove_dir( work_dir ) - # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. - clean_repository_metadata( trans, id, changeset_revisions ) - # Set tool version information for all downloadable changeset revisions. Get the list of changeset revisions from the changelog. - reset_all_tool_versions( trans, id, repo ) - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) - return invalid_file_tups, metadata_dict def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset @@ -938,7 +631,7 @@ message = '' status = 'done' encoded_id = trans.security.encode_id( repository.id ) - repository_clone_url = generate_clone_url( trans, encoded_id ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,11 +9,14 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_file_from_changeset_revision -from galaxy.util.shed_util import get_repository_file_contents, get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk +# TODO: re-factor shed_util to eliminate the following restricted imports +from galaxy.util.shed_util import create_repo_info_dict, generate_clone_url_for_repository_in_tool_shed, generate_message_for_invalid_tools +from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_file_from_changeset_revision, get_repository_file_contents +from galaxy.util.shed_util import get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS -from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path -from galaxy.util.shed_util import to_html_escaped, update_repository, url_join +from galaxy.util.shed_util import open_repository_files_folder, remove_dir, reset_all_metadata_on_repository_in_tool_shed +from galaxy.util.shed_util import reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path, to_html_escaped +from galaxy.util.shed_util import update_repository, url_join from galaxy.tool_shed.encoding_util import * from common import * @@ -639,7 +642,7 @@ else: # The received id is the repository id, so we need to get the id of the user that uploaded the repository. repository_id = kwd.get( 'id', None ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) kwd[ 'f-email' ] = repository.user.email elif operation == "repositories_i_own": # Eliminate the current filters if any exist. @@ -696,7 +699,7 @@ changset_revision_str = 'changeset_revision_' if k.startswith( changset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -710,7 +713,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) # Update repository files for browsing. update_repository( repo ) @@ -771,7 +774,7 @@ operation = kwd[ 'operation' ].lower() if operation == "preview_tools_in_changeset": repository_id = kwd.get( 'id', None ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) repository_metadata = get_latest_repository_metadata( trans, repository.id ) latest_installable_changeset_revision = repository_metadata.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository', @@ -795,7 +798,7 @@ changset_revision_str = 'changeset_revision_' if k.startswith( changset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', @@ -922,7 +925,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) metadata = self.get_metadata( trans, id, repository.tip ) if trans.user and trans.user.email: return trans.fill_template( "/webapps/community/repository/contact_owner.mako", @@ -1033,7 +1036,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository_id = params.get( 'id', None ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) mark_deprecated = util.string_as_bool( params.get( 'mark_deprecated', False ) ) repository.deprecated = mark_deprecated trans.sa_session.add( repository ) @@ -1086,7 +1089,7 @@ def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. params = util.Params( kwd ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) # Allow hgweb to handle the download. This requires the tool shed # server account's .hgrc file to include the following setting: # [web] @@ -1119,7 +1122,7 @@ # The received id is a RepositoryMetadata id, so we have to get the repository id. repository_metadata = get_repository_metadata_by_id( trans, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): @@ -1204,7 +1207,7 @@ # The received id is a RepositoryMetadata id, so we have to get the repository id. repository_metadata = get_repository_metadata_by_id( trans, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): @@ -1309,8 +1312,8 @@ repo_info_dicts = [] for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ): repository_id, changeset_revision = tup - repository_clone_url = generate_clone_url( trans, repository_id ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) metadata = repository_metadata.metadata if not includes_tools and 'tools' in metadata: @@ -1668,7 +1671,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) @@ -1892,7 +1895,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: @@ -1957,7 +1960,7 @@ action='browse_repositories', message='Select a repository to rate', status='error' ) ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', @@ -1985,9 +1988,11 @@ status=status ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - invalid_file_tups, metadata_dict = reset_all_metadata_on_repository( trans, id, **kwd ) + # This method is called only from the ~/templates/webapps/community/repository/manage_repository.mako template. + # It resets all metadata on the complete changelog for a single repository in the tool shed. + invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) if invalid_file_tups: - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict ) status = 'error' else: @@ -2093,7 +2098,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) @@ -2155,7 +2160,7 @@ status=status ) @web.expose def send_to_owner( self, trans, id, message='' ): - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) if not message: message = 'Enter a message' status = 'error' @@ -2205,7 +2210,7 @@ total_alerts_removed = 0 flush_needed = False for repository_id in repository_ids: - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) if repository.email_alerts: email_alerts = from_json_string( repository.email_alerts ) else: @@ -2277,7 +2282,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) changesets = [] for changeset in repo.changelog: @@ -2314,7 +2319,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) ctx = get_changectx_for_changeset( repo, ctx_str ) if ctx is None: @@ -2351,7 +2356,7 @@ status=status ) @web.expose def view_or_manage_repository( self, trans, **kwd ): - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] ) if trans.user_is_admin() or repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', @@ -2366,7 +2371,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -2417,7 +2422,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) - repository = get_repository( trans, id ) + repository = get_repository_in_tool_shed( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) @@ -2499,7 +2504,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) tool_metadata_dict = {} diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -8,7 +8,8 @@ from sqlalchemy.sql.expression import func from common import * from repository import RepositoryGrid -from galaxy.util.shed_util import get_configured_ui +# TODO: re-factor shed_util to eliminate the following restricted imports +from galaxy.util.shed_util import get_configured_ui, get_repository_in_tool_shed from galaxy.util.odict import odict from galaxy import eggs @@ -381,7 +382,7 @@ message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, repository.name ) status = "error" else: - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) # See if there are any reviews for previous changeset revisions that the user can copy. if not create_without_copying and not previous_review_id and has_previous_repository_reviews( trans, repository, changeset_revision ): return trans.response.send_redirect( web.url_for( controller='repository_review', @@ -650,7 +651,7 @@ status = params.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id: - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] @@ -697,7 +698,7 @@ status = params.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) changeset_revision = kwd.get( 'changeset_revision', None ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] @@ -762,7 +763,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) repo = hg.repository( get_configured_ui(), repository.repo_path ) previous_reviews_dict = get_previous_repository_reviews( trans, repository, changeset_revision ) @@ -777,7 +778,7 @@ @web.expose @web.require_login( "view or manage repository" ) def view_or_manage_repository( self, trans, **kwd ): - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] ) if trans.user_is_admin() or repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -3,7 +3,9 @@ from galaxy.model.orm import * from galaxy.datatypes.checkers import * from common import * -from galaxy.util.shed_util import get_configured_ui, reset_tool_data_tables, handle_sample_tool_data_table_conf_file, update_repository +# TODO: re-factor shed_util to eliminate the following restricted imports +from galaxy.util.shed_util import get_configured_ui, get_repository_in_tool_shed, reset_tool_data_tables, handle_sample_tool_data_table_conf_file +from galaxy.util.shed_util import update_repository from galaxy import eggs eggs.require('mercurial') @@ -28,7 +30,7 @@ category_ids = util.listify( params.get( 'category_id', '' ) ) categories = get_categories( trans ) repository_id = params.get( 'repository_id', '' ) - repository = get_repository( trans, repository_id ) + repository = get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) ) diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -10,6 +10,8 @@ from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps from galaxy.model.orm import * from common import * +# TODO: re-factor shed_util to eliminate the following restricted imports +from galaxy.util.shed_util import get_repository_in_tool_shed from galaxy.tool_shed.encoding_util import * class RepoInputDataModule( InputDataModule ): @@ -144,7 +146,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + repository = get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) return trans.fill_template( "/webapps/community/repository/view_workflow.mako", repository=repository, changeset_revision=repository_metadata.changeset_revision, diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -10,8 +10,6 @@ log = logging.getLogger( __name__ ) -MAX_CONTENT_SIZE = 32768 - class InstalledRepositoryGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): @@ -300,7 +298,7 @@ return query class AdminToolshed( AdminGalaxy ): - + installed_repository_grid = InstalledRepositoryGrid() repository_installation_grid = RepositoryInstallationGrid() tool_dependency_grid = ToolDependencyGrid() @@ -309,9 +307,9 @@ @web.require_admin def activate_repository( self, trans, **kwd ): """Activate a repository that was deactivated but not uninstalled.""" - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - repository_clone_url = self.__generate_clone_url( trans, repository ) + repository_clone_url = generate_clone_url_for_installed_repository( trans, repository ) repository.deleted = False repository.status = trans.model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools: @@ -356,7 +354,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', repository=repository, message=message, @@ -380,7 +378,7 @@ action='reset_to_install', **kwd ) ) if operation == "activate or reinstall": - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: if repository.includes_tools: # Only allow selecting a different section in the tool panel if the repository was uninstalled. @@ -440,7 +438,7 @@ @web.require_admin def check_for_updates( self, trans, **kwd ): # Send a request to the relevant tool shed to see if there are any updates. - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ @@ -454,7 +452,7 @@ status = params.get( 'status', 'done' ) remove_from_disk = params.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) - tool_shed_repository = get_repository( trans, kwd[ 'id' ] ) + tool_shed_repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) if relative_install_dir: if tool_path: @@ -819,7 +817,7 @@ status = params.get( 'status', 'done' ) repository_id = kwd[ 'id' ] operation = kwd.get( 'operation', None ) - repository = get_repository( trans, repository_id ) + repository = get_installed_tool_shed_repository( trans, repository_id ) if not repository: return trans.show_error_message( 'Invalid repository specified.' ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: @@ -1237,14 +1235,14 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] - tool_shed_repository = get_repository( trans, repository_id ) + tool_shed_repository = get_installed_tool_shed_repository( trans, repository_id ) no_changes = kwd.get( 'no_changes', '' ) no_changes_checked = CheckboxField.is_checked( no_changes ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section = kwd.get( 'tool_panel_section', '' ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) - repository_clone_url = generate_clone_url( trans, tool_shed_repository ) + repository_clone_url = generate_clone_url_for_installed_repository( trans, tool_shed_repository ) clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) @@ -1395,11 +1393,11 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) metadata = repository.metadata tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) ctx_rev = get_ctx_rev( tool_shed_url, repository.name, repository.owner, repository.installed_changeset_revision ) - repository_clone_url = generate_clone_url( trans, repository ) + repository_clone_url = generate_clone_url_for_installed_repository( trans, repository ) repo_info_dict = create_repo_info_dict( repository, repository.owner, repository_clone_url, @@ -1460,63 +1458,25 @@ status=status ) @web.expose @web.require_admin - def reset_metadata_on_selected_repositories( self, trans, **kwd ): - # TODO: merge this with the similar method in the repository controller. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository_ids = util.listify( kwd.get( 'repository_names_by_owner', None ) ) + def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: - if repository_ids: - successful_count = 0 - unsuccessful_count = 0 - for repository_id in repository_ids: - repository = get_repository( trans, repository_id ) - try: - invalid_file_tups, metadata_dict = self.reset_repository_metadata( trans, - trans.security.encode_id( repository.id ), - resetting_all_repositories=True ) - if invalid_file_tups: - unsuccessful_count += 1 - else: - successful_count += 1 - except Exception, e: - log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) - unsuccessful_count += 1 - message = "Successfully reset metadata on %d %s. " % ( successful_count, - inflector.cond_plural( successful_count, "repository" ) ) - if unsuccessful_count: - message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count, - inflector.cond_plural( unsuccessful_count, - "repository" ) ) - trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='browse_repositories', - message=util.sanitize_text( message ), - status=status ) ) - else: - 'Select at least one repository to on which to reset all metadata.' - status = 'error' - repositories_select_field = SelectField( name='repository_names_by_owner', - multiple=True, - display='checkboxes' ) - for repository in trans.sa_session.query( trans.model.ToolShedRepository ) \ - .filter( trans.model.ToolShedRepository.table.c.uninstalled == False ) \ - .order_by( trans.model.ToolShedRepository.table.c.name, - trans.model.ToolShedRepository.table.c.owner ): - option_label = '%s (%s)' % ( repository.name, repository.owner ) - option_value = trans.security.encode_id( repository.id ) - repositories_select_field.add_option( option_label, option_value ) + kwd[ 'CONTROLLER' ] = GALAXY_ADMIN_TOOL_SHED_CONTROLLER + message, status = reset_metadata_on_selected_repositories( trans, **kwd ) + else: + message = util.restore_text( kwd.get( 'message', '' ) ) + status = kwd.get( 'status', 'done' ) + repositories_select_field = build_repository_ids_select_field( trans, GALAXY_ADMIN_TOOL_SHED_CONTROLLER ) return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, status=status ) @web.expose @web.require_admin - def reset_repository_metadata( self, trans, id, resetting_all_repositories=False ): - """Reset all metadata on the installed tool shed repository.""" - repository = get_repository( trans, id ) + def reset_repository_metadata( self, trans, id ): + """Reset all metadata on a single installed tool shed repository.""" + repository = get_installed_tool_shed_repository( trans, id ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - repository_clone_url = self.__generate_clone_url( trans, repository ) + repository_clone_url = generate_clone_url_for_installed_repository( trans, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata @@ -1533,35 +1493,24 @@ update_in_shed_tool_config( trans.app, repository ) trans.sa_session.add( repository ) trans.sa_session.flush() - if resetting_all_repositories: - log.debug( 'Metadata has been reset on repository %s.' % repository.name ) - else: - message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name - status = 'done' + message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name + status = 'done' else: - if resetting_all_repositories: - log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) - else: - message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name - status = 'done' + message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name + status = 'done' else: - if resetting_all_repositories: - log.debug( 'Error locating installation directory for repository %s.' % repository.name ) - else: - message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name - status = 'error' - if resetting_all_repositories: - return invalid_file_tups, metadata_dict - else: - new_kwd = dict( id=id, message=message, status=status ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repository', - **new_kwd ) ) + message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name + status = 'error' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='manage_repository', + id=id, + message=message, + status=status ) ) @web.expose @web.require_admin def reset_to_install( self, trans, **kwd ): """An error occurred while cloning the repository, so reset everything necessary to enable another attempt.""" - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if kwd.get( 'reset_repository', False ): self.set_repository_attributes( trans, repository, @@ -1596,7 +1545,7 @@ @web.require_admin def set_tool_versions( self, trans, **kwd ): # Get the tool_versions from the tool shed for each tool in the installed change set. - repository = get_repository( trans, kwd[ 'id' ] ) + repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ @@ -1756,7 +1705,7 @@ message = util.restore_text( params.get( 'message', '' ) ) cntrller = params.get( 'cntrller', 'admin_toolshed' ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) + repository = get_installed_tool_shed_repository( trans, id ) metadata = repository.metadata shed_config_dict = repository.get_shed_config_dict( trans.app ) tool_path = shed_config_dict.get( 'tool_path', None ) @@ -1790,7 +1739,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, repository_id ) + repository = get_installed_tool_shed_repository( trans, repository_id ) repository_metadata = repository.metadata shed_config_dict = repository.get_shed_config_dict( trans.app ) tool_metadata = {} @@ -1815,10 +1764,6 @@ tool_lineage=tool_lineage, message=message, status=status ) - def __generate_clone_url( self, trans, repository ): - """Generate the URL for cloning a repository.""" - tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - return url_join( tool_shed_url, 'repos', repository.owner, repository.name ) ## ---- Utility methods ------------------------------------------------------- @@ -1847,9 +1792,6 @@ for option_tup in options: select_field.add_option( option_tup[0], option_tup[1] ) return select_field -def get_repository( trans, id ): - """Get a tool_shed_repository from the database via id""" - return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako --- a/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako +++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako @@ -1,42 +1,10 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> - -<%def name="local_javascripts()"> - <script type="text/javascript"> - function checkAllFields() - { - var chkAll = document.getElementById('checkAll'); - var checks = document.getElementsByTagName('input'); - var boxLength = checks.length; - var allChecked = false; - var totalChecked = 0; - if ( chkAll.checked == true ) - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) - { - checks[i].checked = true; - } - } - } - else - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) - { - checks[i].checked = false - } - } - } - } - </script> -</%def> +<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /><%def name="javascripts()"> ${parent.javascripts()} - ${local_javascripts()} + ${common_misc_javascripts()} </%def> %if message: @@ -50,13 +18,13 @@ <div class="toolForm"><div class="toolFormTitle">Reset all metadata on each selected tool shed repository</div> - <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" method="post" > + <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_installed_repositories' )}" method="post" ><div class="form-row"> Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAll" name=select_all_repositories_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_repositories_checkbox value="true"/><b>Select/unselect all repositories</b> + <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b></div><div style="clear: both"></div><div class="form-row"> diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -55,7 +55,7 @@ <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}">Reset selected metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}">Reset selected metadata</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a> diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako --- a/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako +++ b/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako @@ -1,42 +1,10 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> - -<%def name="local_javascripts()"> - <script type="text/javascript"> - function checkAllFields() - { - var chkAll = document.getElementById('checkAll'); - var checks = document.getElementsByTagName('input'); - var boxLength = checks.length; - var allChecked = false; - var totalChecked = 0; - if ( chkAll.checked == true ) - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) - { - checks[i].checked = true; - } - } - } - else - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) - { - checks[i].checked = false - } - } - } - } - </script> -</%def> +<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /><%def name="javascripts()"> ${parent.javascripts()} - ${local_javascripts()} + ${common_misc_javascripts()} </%def> %if message: @@ -51,13 +19,13 @@ <div class="toolForm"><div class="toolFormTitle">Reset all metadata on each selected repository</div> - <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}" method="post" > + <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}" method="post" ><div class="form-row"> Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAll" name=select_all_repositories_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_repositories_checkbox value="true"/><b>Select/unselect all repositories</b> + <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b></div><div style="clear: both"></div><div class="form-row"> diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/community/common/common.mako --- a/templates/webapps/community/common/common.mako +++ b/templates/webapps/community/common/common.mako @@ -1,3 +1,36 @@ +<%def name="common_misc_javascripts()"> + <script type="text/javascript"> + function checkAllFields( name ) + { + var chkAll = document.getElementById( 'checkAll' ); + var checks = document.getElementsByTagName( 'input' ); + var boxLength = checks.length; + var allChecked = false; + var totalChecked = 0; + if ( chkAll.checked == true ) + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( name ) != -1 ) + { + checks[i].checked = true; + } + } + } + else + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( name ) != -1 ) + { + checks[i].checked = false + } + } + } + } + </script> +</%def> + <%def name="escape_html_add_breaks( value )"><% from galaxy import eggs diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -77,8 +77,8 @@ <%def name="render_clone_str( repository )"><% - from galaxy.webapps.community.controllers.common import generate_clone_url - clone_str = generate_clone_url( trans, trans.security.encode_id( repository.id ) ) + from galaxy.util.shed_util import generate_clone_url_for_repository_in_tool_shed + clone_str = generate_clone_url_for_repository_in_tool_shed( trans, repository ) %> hg clone <a href="${clone_str}">${clone_str}</a></%def> diff -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -75,7 +75,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=installing_repository_ids )}" target="galaxy_main">Monitor installing tool shed repositories</a></div> %endif %if installed_repositories: - <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" target="galaxy_main">Reset metadata for tool shed repositories</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_installed_repositories' )}" target="galaxy_main">Reset metadata for tool shed repositories</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> %endif </div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Download eggs from Galaxy resources in EC2.
by Bitbucket 26 Oct '12

26 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b2975e2fa684/ changeset: b2975e2fa684 user: natefoo date: 2012-10-26 18:56:23 summary: Download eggs from Galaxy resources in EC2. affected #: 1 file diff -r bfbd456ebbbe7cff89ffda39091d37ffdbdf2d2a -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -7,7 +7,7 @@ ; [general] -repository = http://eggs.g2.bx.psu.edu +repository = http://eggs.galaxyproject.org ; these eggs must be scrambled for your local environment no_auto = pbs_python DRMAA_python Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Log the underlying cause of job output collection failure in the drmaa runner.
by Bitbucket 26 Oct '12

26 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bfbd456ebbbe/ changeset: bfbd456ebbbe user: natefoo date: 2012-10-26 16:55:46 summary: Log the underlying cause of job output collection failure in the drmaa runner. affected #: 1 file diff -r 720b4067ab5e5b617569278155ab21216c0de176 -r bfbd456ebbbe7cff89ffda39091d37ffdbdf2d2a lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -353,11 +353,11 @@ # The exit code should only be 8 bits, but read more anyway exit_code_str = ecfh.read(32) which_try = (self.app.config.retry_job_output_collection + 1) - except: + except Exception, e: if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' - log.debug( stderr ) + log.warning( '%s: %s' % ( stderr, str( e ) ) ) else: time.sleep(1) which_try += 1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 26 Oct '12

26 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5c3675b6d1bd/ changeset: 5c3675b6d1bd user: fubar date: 2012-10-26 07:00:13 summary: Fix parameters for fastqc to work properly with bam and with a contaminants file Been b0rken for a long time - probably not much used.. affected #: 3 files diff -r f156b9e144437e541127009c2a32efc1019af5c7 -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -911,7 +911,7 @@ self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True - self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) + self.usecolnames = string_as_bool( elem.get( "use_header_names", True )) # much easier for the user - make default if not overridden def from_html( self, value, trans=None, context={} ): """ diff -r f156b9e144437e541127009c2a32efc1019af5c7 -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -15,7 +15,7 @@ </command><inputs><param format="tabular" name="input" type="data" label="Sort Query" /> - <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> + <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/><param name="style" type="select" label="with flavor"><option value="num">Numerical sort</option><option value="alpha">Alphabetical sort</option> diff -r f156b9e144437e541127009c2a32efc1019af5c7 -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -51,9 +51,9 @@ fastq = os.path.basename(self.opts.input) cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir] if self.opts.informat in ['sam','bam']: - cl.append('-f %s' % self.opts.informat) + cl.append('--f=%s' % self.opts.informat) if self.opts.contaminants <> None : - cl.append('-c %s' % self.opts.contaminants) + cl.append('--contaminants=%s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) https://bitbucket.org/galaxy/galaxy-central/changeset/720b4067ab5e/ changeset: 720b4067ab5e user: fubar date: 2012-10-26 07:03:10 summary: Revert use_header_names to default false - breaks a couple of existing tests - would need to repair those too. affected #: 1 file diff -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 -r 720b4067ab5e5b617569278155ab21216c0de176 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -911,7 +911,7 @@ self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True - self.usecolnames = string_as_bool( elem.get( "use_header_names", True )) # much easier for the user - make default if not overridden + self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) def from_html( self, value, trans=None, context={} ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for determining the extraction directory for tool dependency tarballs when installing tool dependencies along with tool shed repositories.
by Bitbucket 25 Oct '12

25 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f156b9e14443/ changeset: f156b9e14443 user: greg date: 2012-10-25 20:46:57 summary: Fix for determining the extraction directory for tool dependency tarballs when installing tool dependencies along with tool shed repositories. affected #: 2 files diff -r 42eedc24fdd62034ce039bf56b2bbb0b382c63e0 -r f156b9e144437e541127009c2a32efc1019af5c7 lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py @@ -1,18 +1,6 @@ import os, shutil, tarfile, urllib2, zipfile from galaxy.datatypes.checkers import * -def zipfile_ok( path_to_archive ): - """ - This function is a bit pedantic and not functionally necessary. It checks whether there is no file pointing outside of the extraction, - because ZipFile.extractall() has some potential security holes. See python zipfile documentation for more details. - """ - basename = os.path.realpath( os.path.dirname( path_to_archive ) ) - zip_archive = zipfile.ZipFile( path_to_archive ) - for member in zip_archive.namelist(): - member_path = os.path.realpath( os.path.join( basename, member ) ) - if not member_path.startswith( basename ): - return False - return True def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ): env_var_name = elem.get( 'name', 'PATH' ) env_var_action = elem.get( 'action', 'prepend_to' ) @@ -103,6 +91,7 @@ os.makedirs( destination_directory ) shutil.move( source_file, destination_directory ) def tar_extraction_directory( file_path, file_name ): + """Try to return the correct extraction directory.""" file_name = file_name.strip() extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.zip' ] for extension in extensions: @@ -111,8 +100,8 @@ if os.path.exists( os.path.abspath( os.path.join( file_path, dir_name ) ) ): return dir_name if os.path.exists( os.path.abspath( os.path.join( file_path, file_name ) ) ): - return os.path.abspath( os.path.join( file_path, file_name ) ) - raise ValueError( 'Could not find directory %s' % os.path.abspath( os.path.join( file_path, file_name[ :-len( extension ) ] ) ) ) + return os.path.abspath( file_path ) + raise ValueError( 'Could not find path to file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) def url_download( install_dir, downloaded_file_name, download_url ): file_path = os.path.join( install_dir, downloaded_file_name ) src = None @@ -138,3 +127,15 @@ if os.path.isdir( os.path.join( file_path, files[ 0 ] ) ): return os.path.abspath( os.path.join( file_path, files[ 0 ] ) ) raise ValueError( 'Could not find directory for the extracted file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) +def zipfile_ok( path_to_archive ): + """ + This function is a bit pedantic and not functionally necessary. It checks whether there is no file pointing outside of the extraction, + because ZipFile.extractall() has some potential security holes. See python zipfile documentation for more details. + """ + basename = os.path.realpath( os.path.dirname( path_to_archive ) ) + zip_archive = zipfile.ZipFile( path_to_archive ) + for member in zip_archive.namelist(): + member_path = os.path.realpath( os.path.join( basename, member ) ) + if not member_path.startswith( basename ): + return False + return True diff -r 42eedc24fdd62034ce039bf56b2bbb0b382c63e0 -r f156b9e144437e541127009c2a32efc1019af5c7 lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -79,7 +79,7 @@ if not os.path.exists( dir ): os.makedirs( dir ) # The package has been down-loaded, so we can now perform all of the actions defined for building it. - with lcd( dir ): + with lcd( dir ): for action_tup in actions[ 1: ]: action_type, action_dict = action_tup current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Pack workflow editor javascript to be compatible with changes in pull request #76
by Bitbucket 25 Oct '12

25 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/42eedc24fdd6/ changeset: 42eedc24fdd6 user: dannon date: 2012-10-25 19:52:26 summary: Pack workflow editor javascript to be compatible with changes in pull request #76 affected #: 1 file diff -r 1136605c015d0e28ba42c9ad83f860652ee453a4 -r 42eedc24fdd62034ce039bf56b2bbb0b382c63e0 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b,a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0&&g==workflow.active_node){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_paths.attributes.image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b,a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0&&g==workflow.active_node){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_paths.attributes.image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification 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commit/galaxy-central: inithello: Updated migration script to reference repository with correct use of tool dependency tag sets.
by Bitbucket 25 Oct '12

25 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1136605c015d/ changeset: 1136605c015d user: inithello date: 2012-10-25 19:25:39 summary: Updated migration script to reference repository with correct use of tool dependency tag sets. affected #: 1 file diff -r b121409702081725920cec548eea991b1bbe6a6f -r 1136605c015d0e28ba42c9ad83f860652ee453a4 scripts/migrate_tools/0006_tools.xml --- a/scripts/migrate_tools/0006_tools.xml +++ b/scripts/migrate_tools/0006_tools.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"> - <repository name="picard" description="Galaxy wrappers for captain picard." changeset_revision="1cd7f3b42609"> + <repository name="picard" description="Galaxy wrappers for the Picard SAM/BAM manipulation tools." changeset_revision="e0232cbac965"><tool id="picard_FastqToSam" version="1.56.0" file="picard_FastqToSam.xml" /><tool id="picard_SamToFastq" version="1.56.1" file="picard_SamToFastq.xml" /><tool id="picard_BamIndexStats" version="1.56.0" file="picard_BamIndexStats.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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