galaxy-commits October 2014

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174 discussions

[galaxyproject/usegalaxy-playbook] 3de753: Main: Schedule wig_to_bigWig and bed_to_bigBed mem...
by GitHub 23 Oct '14

23 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3de7534001170053915202c7e9ef50301a7b5eaf https://github.com/galaxyproject/usegalaxy-playbook/commit/3de7534001170053… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-22 (Wed, 22 Oct 2014) Changed paths: A files/galaxy/usegalaxy.org/dynamic_rules/single_dynamic_memory.py M production/group_vars/galaxyservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Main: Schedule wig_to_bigWig and bed_to_bigBed memory dynamically.

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[galaxyproject/usegalaxy-playbook] 007e0a: Test: Schedule wig_to_bigWig and bed_to_bigBed mem...
by GitHub 23 Oct '14

23 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 007e0a78e74a558db22e1fc62fc1d8a81626fc33 https://github.com/galaxyproject/usegalaxy-playbook/commit/007e0a78e74a558d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-22 (Wed, 22 Oct 2014) Changed paths: A files/galaxy/test.galaxyproject.org/dynamic_rules/single_dynamic_memory.py M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Test: Schedule wig_to_bigWig and bed_to_bigBed memory dynamically.

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commit/galaxy-central: martenson: updated sphinx documentation: added managers; added new API controllers; cleanup
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f25e90163bbd/ Changeset: f25e90163bbd User: martenson Date: 2014-10-22 21:55:45+00:00 Summary: updated sphinx documentation: added managers; added new API controllers; cleanup Affected #: 4 files diff -r 7c66e468c6024b2e17a70ffadae0ad080b174c68 -r f25e90163bbd16626ce9adf7854ff493c79b469d doc/source/conf.py --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -11,7 +11,7 @@ # All configuration values have a default; values that are commented out # serve to show the default. -import sys, os +import sys, os, datetime ####### REQUIRED GALAXY INCLUDES @@ -40,7 +40,7 @@ templates_path = ['_templates'] #configure default autodoc's action -autodoc_default_flags = ['members', 'undoc-members'] +autodoc_default_flags = [ 'members', 'undoc-members', 'show-inheritance' ] # The suffix of source filenames. source_suffix = '.rst' @@ -53,7 +53,7 @@ # General information about the project. project = u'Galaxy Code' -copyright = u'2012, Galaxy Team' +copyright = str( datetime.datetime.now().year ) + u', Galaxy Team' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the diff -r 7c66e468c6024b2e17a70ffadae0ad080b174c68 -r f25e90163bbd16626ce9adf7854ff493c79b469d doc/source/lib/galaxy.managers.rst --- /dev/null +++ b/doc/source/lib/galaxy.managers.rst @@ -0,0 +1,92 @@ +managers Package +================== + +:mod:`managers` Package +------------------------- + +.. automodule:: galaxy.managers + + +:mod:`api_keys` Module +------------------------------ + +.. automodule:: galaxy.managers.api_keys + + +:mod:`base` Module +------------------------------ + +.. automodule:: galaxy.managers.base + + +:mod:`citations` Module +------------------------------ + +.. automodule:: galaxy.managers.citations + + +:mod:`collections` Module +------------------------------ + +.. automodule:: galaxy.managers.collections + + +:mod:`collections_util` Module +------------------------------ + +.. automodule:: galaxy.managers.collections_util + + +:mod:`context` Module +------------------------------ + +.. automodule:: galaxy.managers.context + + +:mod:`folders` Module +------------------------------ + +.. automodule:: galaxy.managers.folders + + +:mod:`hdas` Module +------------------------------ + +.. automodule:: galaxy.managers.hdas + + +:mod:`histories` Module +------------------------------ + +.. automodule:: galaxy.managers.histories + + +:mod:`lddas` Module +------------------------------ + +.. automodule:: galaxy.managers.lddas + + +:mod:`libraries` Module +------------------------------ + +.. automodule:: galaxy.managers.libraries + + +:mod:`roles` Module +------------------------------ + +.. automodule:: galaxy.managers.roles + + +:mod:`tags` Module +------------------------------ + +.. automodule:: galaxy.managers.tags + + +:mod:`workflows` Module +------------------------------ + +.. automodule:: galaxy.managers.workflows + :undoc-members: diff -r 7c66e468c6024b2e17a70ffadae0ad080b174c68 -r f25e90163bbd16626ce9adf7854ff493c79b469d doc/source/lib/galaxy.rst --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -38,6 +38,7 @@ galaxy.forms galaxy.jobs galaxy.model + galaxy.managers galaxy.objectstore galaxy.openid galaxy.quota @@ -51,4 +52,3 @@ galaxy.web galaxy.webapps galaxy.workflow - diff -r 7c66e468c6024b2e17a70ffadae0ad080b174c68 -r f25e90163bbd16626ce9adf7854ff493c79b469d doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -3,16 +3,16 @@ Background ========== -In addition to being accessible through a web interface, Galaxy can now also be +In addition to being accessible through a web interface, Galaxy can 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 + workflows whenever data is ready. - Running a workflow against multiple datasets (which can be done with the - web interface, but is tedious) + web interface, but is tedious). - When the analysis involves complex control, such as looping and branching. @@ -132,7 +132,7 @@ description: API Test Library name: api_test - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents Collection Members ------------------ /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 @@ -205,208 +205,6 @@ The request and response format should be considered alpha and are subject to change. -API Return Codes and Formats -================== - -A set of error codes for API requests is being established and will be -documented here. This is a long-term project however so stayed tuned. - -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:`item_tags` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.item_tags - :members: - :undoc-members: - :show-inheritance: - -:mod:`lda_datasets` Module --------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.lda_datasets - :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: - - API Design Guidelines ===================== @@ -418,26 +216,34 @@ - API functionality should include docstring documentation for consumption by readthedocs.org. - - Developers should familarize themselves with the HTTP status code definitions + - Developers should familiarize themselves with the HTTP status code definitions http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html. The API responses should properly set the status code according to the result - in particular 2XX responses should be used for successful requests, 4XX for various - kinds of client errors, and 5XX for errors on the server side. + kinds of client errors, and 5XX for the errors on the server side. - If there is an error processing some part of request (one item in a list for instance), the status code should be set to reflect the error and the partial result may or may not be returned depending on the controller - this behavior should be documented. - - (TODO) API methods should throw a finite number of exceptions (defined in) - `galaxy.exceptions` and these should subclass `MessageException` and not - paste/wsgi HTTP exceptions. When possible, the framework itself should be - responsible catching these exceptions, setting the status code, and - building an error response. + - API methods should throw a finite number of exceptions + (defined in :doc:`galaxy.exceptions`) and these should subclass + `MessageException` and not paste/wsgi HTTP exceptions. When possible, + the framework itself should be responsible catching these exceptions, + setting the status code, and building an error response. - Error responses should not consist of plain text strings - they should be - dictionaries describing the error and containing the following keys (TODO: - spell out nature of this.) Various error conditions (once a format has - been chosen and framework to enforce it in place) should be spelled out - in this document. - - Backward compatibility is important and should maintained when possible. + dictionaries describing the error and containing the following:: + + { + "status_code": 400, + "err_code": 400007, + "err_msg": "Request contained invalid parameter, action could not be completed.", + "type": "error", + "extra_error_info": "Extra information." + } + + Various error conditions (once a format has been chosen and framework to + enforce it in place) should be spelled out in this document. + - Backward compatibility is important and should be maintained when possible. If changing behavior in a non-backward compatibile way please ensure one of the following holds - there is a strong reason to believe no consumers depend on a behavior, the behavior is effectively broken, or the API @@ -448,7 +254,8 @@ - Functionality should not be copied and pasted between controllers - consider refactoring functionality into associated classes or short of - that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance). + that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance) + or into Managers (:doc:`galaxy.managers`). - API additions are more permanent changes to Galaxy than many other potential changes and so a second opinion on API changes should be sought. (Consider a pull request!) @@ -457,16 +264,252 @@ `test/functional/api`. (Once such a framework is in place - it is not right now). - Changes to reflect modifications to the API should be pushed upstream to - the BioBlend project possible. + the BioBlend project if possible. Longer term goals/notes. - It would be advantageous to have a clearer separation of anonymous and admin handling functionality. - If at some point in the future, functionality needs to be added that - breaks backward compatibility in a significant way to a compontent used by - the community should be alerted - a "dev" variant of the API will be - established and the community should be alerted and given a timeframe - for when the old behavior will be replaced with the new behavior. + breaks backward compatibility in a significant way to a component used by + the community - a "dev" variant of the API will be established and + the community should be alerted and given a timeframe for when the old + behavior will be replaced with the new behavior. - Consistent standards for range-based requests, batch requests, filtered requests, etc... should be established and documented here. + +API Controllers +=============== + +Galaxy offers the following API controllers: + +:mod:`annotations` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.annotations + +:mod:`authenticate` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.authenticate + +:mod:`configuration` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.configuration + +:mod:`dataset_collections` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.dataset_collections + + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + + +:mod:`datatypes` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datatypes + + +:mod:`extended_metadata` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.extended_metadata + + +:mod:`folder_contents` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + + +:mod:`folders` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.forms + + +:mod:`ftp_files` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.ftp_files + + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + + +:mod:`group_roles` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + + +:mod:`group_users` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups + + +:mod:`histories` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + + +:mod:`history_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + + +:mod:`item_tags` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.item_tags + + +:mod:`job_files` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.job_files + + +:mod:`jobs` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.jobs + + +:mod:`lda_datasets` Module +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.lda_datasets + + +:mod:`libraries` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + + +:mod:`library_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + + +:mod:`metrics` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.metrics + + +:mod:`page_revisions` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.page_revisions + + +:mod:`pages` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.pages + + +:mod:`provenance` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.provenance + + +:mod:`quotas` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.quotas + + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + + +:mod:`roles` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.roles + + +:mod:`samples` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + + +:mod:`search` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.search + + +:mod:`tool_data` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tool_data + + +:mod:`tool_shed_repositories` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories + + +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tools + + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.users + + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + 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: martenson: data libs API documentation
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c66e468c602/ Changeset: 7c66e468c602 User: martenson Date: 2014-10-22 18:08:57+00:00 Summary: data libs API documentation Affected #: 1 file diff -r 2fd74c3386c8934297d2b85249539a17353d8269 -r 7c66e468c6024b2e17a70ffadae0ad080b174c68 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -370,8 +370,8 @@ :param encoded_dataset_id: the encoded id of the dataset to change :type encoded_dataset_id: an encoded id string + :returns: dict containing information about the dataset :rtype: dictionary - :returns: dict containing information about the dataset """ undelete = util.string_as_bool( kwd.get( 'undelete', False ) ) try: @@ -400,16 +400,34 @@ @expose_api def load( self, trans, **kwd ): """ - Load dataset from the given source into the library. + load( self, trans, **kwd ): + * POST /api/libraries/datasets + Load dataset from the given source into the library. + Source can be: + user directory - root folder specified in galaxy.ini as "$user_library_import_dir" + example path: path/to/galaxy/$user_library_import_dir/user(a)example.com/{user can browse everything here} + the folder with the user login has to be created beforehand + (admin)import directory - root folder specified in galaxy ini as "$library_import_dir" + example path: path/to/galaxy/$library_import_dir/{admin can browse everything here} + (admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini + + :param encoded_folder_id: the encoded id of the folder to import dataset(s) to + :type encoded_folder_id: an encoded id string + :param source: source the datasets should be loaded form + :type source: str + :param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy + while linking is set to True all symlinks will be resolved _once_ + :type link_data: bool + :param preserve_dirs: flag whether to preserve the directory structure when importing dir + if False only datasets will be imported + :type preserve_dirs: bool + :param file_type: file type of the loaded datasets, defaults to 'auto' (autodetect) + :type file_type: str + :param dbkey: dbkey of the loaded genome, defaults to '?' (unknown) + :type dbkey: str - :param encoded_folder_id: the encoded id of the folder to import dataset to - :type encoded_folder_id: an encoded id string - :param source: source of the dataset to be loaded - :type source: str - :param link_data: flag whether to link the dataset to data or copy it to Galaxy - :type link_data: bool - :param preserve_dirs: flag whether to preserver directory structure when importing dir - :type preserve_dirs: bool + :returns: dict containing information about the created upload job + :rtype: dictionary """ kwd[ 'space_to_tab' ] = 'False' @@ -443,9 +461,7 @@ if user_base_dir is None: raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' ) full_dir = os.path.join( user_base_dir, user_login ) - # path_to_root_import_folder = None if not path.lower().startswith( full_dir.lower() ): - # path_to_root_import_folder = path path = os.path.join( full_dir, path ) if not os.path.exists( path ): raise exceptions.RequestParameterInvalidException( 'Given path does not exist on the host.' ) 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: martenson: data libs: hide share button, render first page by default, fix admin imports from import_dir, fix height of folder item row changing on hover
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2fd74c3386c8/ Changeset: 2fd74c3386c8 User: martenson Date: 2014-10-22 17:39:39+00:00 Summary: data libs: hide share button, render first page by default, fix admin imports from import_dir, fix height of folder item row changing on hover Affected #: 12 files diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -504,7 +504,7 @@ tmpl_array.push(' <% if (item.get("can_user_manage")) { %>'); tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push(' <% } %>'); diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js @@ -97,7 +97,7 @@ var library_page_size = prompt( 'How many libraries per page do you want to see?', Galaxy.libraries.preferences.get( 'library_page_size' ) ); if ( ( library_page_size != null ) && ( library_page_size == parseInt( library_page_size ) ) ) { Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( library_page_size ) } ); - Galaxy.libraries.libraryListView.render(); + Galaxy.libraries.libraryListView.render( { show_page: 1 } ); } }, diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -414,7 +414,6 @@ kwd[ 'space_to_tab' ] = 'False' kwd[ 'to_posix_lines' ] = 'True' - kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' ) kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' ) kwd[' link_data_only' ] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files' @@ -436,9 +435,8 @@ raise exceptions.AdminRequiredException( 'Only admins can import from importdir.' ) if not trans.app.config.library_import_dir: raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow admins to import into library from importdir.' ) - user_base_dir = trans.app.config.library_import_dir - - + import_base_dir = trans.app.config.library_import_dir + path = os.path.join( import_base_dir, path ) if source in [ 'userdir_file', 'userdir_folder' ]: user_login = trans.user.email user_base_dir = trans.app.config.user_library_import_dir @@ -472,9 +470,11 @@ library_bunch = upload_common.handle_library_params( trans, {}, trans.security.encode_id( folder.id ) ) abspath_datasets = [] kwd[ 'filesystem_paths' ] = path + if source in [ 'importdir_folder' ]: + kwd[ 'filesystem_paths' ] = os.path.join( import_base_dir, path ) params = util.Params( kwd ) # user wants to import one file only - if source == "userdir_file": + if source in [ "userdir_file", "importdir_file" ]: file = os.path.abspath( path ) abspath_datasets.append( trans.webapp.controllers[ 'library_common' ].make_library_uploaded_dataset( trans, 'api', params, os.path.basename( file ), file, 'server_dir', library_bunch ) ) @@ -482,14 +482,14 @@ if source == "userdir_folder": uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( trans, 'api', params, library_bunch, 200, '' ) - uploaded_datasets = uploaded_datasets_bunch[0] + uploaded_datasets = uploaded_datasets_bunch[ 0 ] if uploaded_datasets is None: raise exceptions.ObjectNotFound( 'Given folder does not contain any datasets.' ) for ud in uploaded_datasets: ud.path = os.path.abspath( ud.path ) abspath_datasets.append( ud ) - # user wants to import from path (admins only) - if source == "admin_path": + # user wants to import from path + if source in [ "admin_path", "importdir_folder" ]: # validate the path is within root uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( trans, 'api', params, library_bunch, 200, '' ) diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -504,7 +504,7 @@ tmpl_array.push(' <% if (item.get("can_user_manage")) { %>'); tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push(' <% } %>'); diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -168,11 +168,11 @@ this.$el.find('#first_folder_item').after(rowView.el); - $('.library-row').hover(function() { - $(this).find('.show_on_hover').show(); - }, function () { - $(this).find('.show_on_hover').hide(); - }); + // $('.library-row').hover(function() { + // $(this).find('.show_on_hover').show(); + // }, function () { + // $(this).find('.show_on_hover').hide(); + // }); }, /** diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -97,7 +97,7 @@ var library_page_size = prompt( 'How many libraries per page do you want to see?', Galaxy.libraries.preferences.get( 'library_page_size' ) ); if ( ( library_page_size != null ) && ( library_page_size == parseInt( library_page_size ) ) ) { Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( library_page_size ) } ); - Galaxy.libraries.libraryListView.render(); + Galaxy.libraries.libraryListView.render( { show_page: 1 } ); } }, diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sortColumnClicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll();this.checkEmptiness()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el)},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sortColumnClicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll();this.checkEmptiness()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/packed/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"showLibraryModal","click #include_deleted_chk":"includeDeletedChecked","click #page_size_prompt":"showPageSizePrompt"},initialize:function(d){this.options=_.defaults(this.options||{},d);this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},renderPaginator:function(e){this.options=_.extend(this.options,e);var d=this.templatePaginator();this.$el.find("#library_paginator").html(d({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},showLibraryModal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.createNewLibrary()},Close:function(){d.modal.hide()}}})},createNewLibrary:function(){var f=this.serializeNewLibrary();if(this.valdiateNewLibrary(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clearLibraryModal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},showPageSizePrompt:function(){var d=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));if((d!=null)&&(d==parseInt(d))){Galaxy.libraries.preferences.set({library_page_size:parseInt(d)});Galaxy.libraries.libraryListView.render()}},clearLibraryModal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},valdiateNewLibrary:function(d){return d.name!==""},includeDeletedChecked:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <form class="form-inline" role="form">');tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div class="checkbox" style="height: 20px;">');tmpl_array.push(" <label>");tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>');tmpl_array.push(" </label>");tmpl_array.push(" </div>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="library_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </form>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page" id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"showLibraryModal","click #include_deleted_chk":"includeDeletedChecked","click #page_size_prompt":"showPageSizePrompt"},initialize:function(d){this.options=_.defaults(this.options||{},d);this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},renderPaginator:function(e){this.options=_.extend(this.options,e);var d=this.templatePaginator();this.$el.find("#library_paginator").html(d({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},showLibraryModal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.createNewLibrary()},Close:function(){d.modal.hide()}}})},createNewLibrary:function(){var f=this.serializeNewLibrary();if(this.valdiateNewLibrary(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clearLibraryModal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},showPageSizePrompt:function(){var d=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));if((d!=null)&&(d==parseInt(d))){Galaxy.libraries.preferences.set({library_page_size:parseInt(d)});Galaxy.libraries.libraryListView.render({show_page:1})}},clearLibraryModal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},valdiateNewLibrary:function(d){return d.name!==""},includeDeletedChecked:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <form class="form-inline" role="form">');tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div class="checkbox" style="height: 20px;">');tmpl_array.push(" <label>");tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>');tmpl_array.push(" </label>");tmpl_array.push(" </div>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="library_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </form>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page" id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1322,6 +1322,7 @@ .ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} .ui-select-multiple{height:100% !important;width:100% !important} .libraryRow{background-color:#ebd9b2} +tr{height:32px} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} div.libraryItemBody{padding:4px 4px 2px 4px} diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -1,6 +1,7 @@ a{text-decoration:underline} label{font-weight:normal} .libraryRow{background-color:#ebd9b2} +tr{height:32px} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} div.libraryItemBody{padding:4px 4px 2px 4px} diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -5,6 +5,9 @@ background-color: @table-heading-bg; } +tr{ + height: 32px; +} .datasetHighlighted { background-color: @table-bg-accent; } 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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[galaxyproject/usegalaxy-playbook] c364a1: Update Main, update Main Pulsar, add nagios checks...
by GitHub 22 Oct '14

22 Oct '14

1 0

[galaxyproject/usegalaxy-playbook] 8d5aad: Get changed mutable configs on Test
by GitHub 22 Oct '14

22 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8d5aada303c061abe34e37fb7d1dd7d2928f7c4c https://github.com/galaxyproject/usegalaxy-playbook/commit/8d5aada303c061ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-22 (Wed, 22 Oct 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Get changed mutable configs on Test

1 0

[galaxyproject/usegalaxy-playbook] c24a01: Update Test/Pulsar.
by GitHub 21 Oct '14

21 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c24a01d929076abe2155c36c45b6cfed040a5171 https://github.com/galaxyproject/usegalaxy-playbook/commit/c24a01d929076abe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-21 (Tue, 21 Oct 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Test/Pulsar.

1 0

commit/galaxy-central: jmchilton: Require pyyaml egg before using.
by commits-noreply＠bitbucket.org 21 Oct '14

21 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/28a24d7d3e84/ Changeset: 28a24d7d3e84 User: jmchilton Date: 2014-10-21 16:32:57+00:00 Summary: Require pyyaml egg before using. Thanks @natefoo. Affected #: 1 file diff -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -6,6 +6,8 @@ from galaxy.util.bunch import Bunch from galaxy import web +from galaxy import eggs +eggs.require("PyYAML") import yaml from galaxy.managers import api_keys 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: natefoo: Update tag latest_2014.10.06 for changeset a7b2aabb27ff
by commits-noreply＠bitbucket.org 21 Oct '14

21 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1e1beeb5322/ Changeset: d1e1beeb5322 Branch: stable User: natefoo Date: 2014-10-21 13:00:16+00:00 Summary: Update tag latest_2014.10.06 for changeset a7b2aabb27ff Affected #: 1 file diff -r a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 -r d1e1beeb532239250396dd8fbdc0156508c6744e .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e1404e285ccb9e52bd09c5827934cd0da1974acc latest_2014.10.06 +a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 latest_2014.10.06 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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