- galaxy-commits - lists.galaxyproject.org

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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