galaxy-commits April 2014

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f29e27d4592/ Changeset: 2f29e27d4592 Branch: remove-stale-ignored User: trevorw Date: 2014-04-11 05:54:34 Summary: remove misc files that slipped past hgignore Affected #: 2 files diff -r 165927888055c164e493a948e05d10c00d018458 -r 2f29e27d45921a466c274fe7470499220865d63b doc/source/lib/galaxy.webapps.galaxy.api.rst~ --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst~ +++ /dev/null @@ -1,179 +0,0 @@ -api Package -=========== - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`folder_contents` Module ------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.folder_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`folders` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.folders - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.genomes - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_roles` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_users` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_users - :members: - :undoc-members: - :show-inheritance: - -:mod:`groups` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.groups - :members: - :undoc-members: - :show-inheritance: - -:mod:`histories` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.histories - :members: - :undoc-members: - :show-inheritance: - -:mod:`history_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`libraries` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.libraries - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`permissions` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.permissions - :members: - :undoc-members: - :show-inheritance: - -:mod:`quotas` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.quotas - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_types` Module ---------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.request_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`roles` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`samples` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.samples - :members: - :undoc-members: - :show-inheritance: - -:mod:`tools` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tools - :members: - :undoc-members: - :show-inheritance: - -:mod:`users` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.users - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualizations` Module ----------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflows` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.workflows - :members: - :undoc-members: - :show-inheritance: - diff -r 165927888055c164e493a948e05d10c00d018458 -r 2f29e27d45921a466c274fe7470499220865d63b static/jqtouch/.DS_Store Binary file static/jqtouch/.DS_Store has changed https://bitbucket.org/galaxy/galaxy-central/commits/ac7fc8911184/ Changeset: ac7fc8911184 User: dannon Date: 2014-04-11 15:04:46 Summary: Merged in trevorw/galaxy-central-t/remove-stale-ignored (pull request #364) remove misc files that slipped past hgignore Affected #: 2 files diff -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 -r ac7fc8911184064056255224711031153f9421db doc/source/lib/galaxy.webapps.galaxy.api.rst~ --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst~ +++ /dev/null @@ -1,179 +0,0 @@ -api Package -=========== - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`folder_contents` Module ------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.folder_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`folders` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.folders - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.genomes - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_roles` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_users` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_users - :members: - :undoc-members: - :show-inheritance: - -:mod:`groups` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.groups - :members: - :undoc-members: - :show-inheritance: - -:mod:`histories` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.histories - :members: - :undoc-members: - :show-inheritance: - -:mod:`history_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`libraries` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.libraries - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`permissions` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.permissions - :members: - :undoc-members: - :show-inheritance: - -:mod:`quotas` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.quotas - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_types` Module ---------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.request_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`roles` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`samples` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.samples - :members: - :undoc-members: - :show-inheritance: - -:mod:`tools` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tools - :members: - :undoc-members: - :show-inheritance: - -:mod:`users` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.users - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualizations` Module ----------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflows` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.workflows - :members: - :undoc-members: - :show-inheritance: - diff -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 -r ac7fc8911184064056255224711031153f9421db static/jqtouch/.DS_Store Binary file static/jqtouch/.DS_Store has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/be7d6bac2fb1/ Changeset: be7d6bac2fb1 User: nsoranzo Date: 2014-04-10 18:22:32 Summary: Remove unused method. Affected #: 1 file diff -r 165927888055c164e493a948e05d10c00d018458 -r be7d6bac2fb115bad61d92db0efeef24deafc73a lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -152,48 +152,6 @@ # -- Helper methods -- # - def _run_tool( self, trans, tool_id, target_dataset_id, **kwargs ): - """ - Run a tool. This method serves as a general purpose way to run tools asynchronously. - """ - - # - # Set target history (the history that tool will use for outputs) using - # target dataset. If user owns dataset, put new data in original - # dataset's history; if user does not own dataset (and hence is accessing - # dataset via sharing), put new data in user's current history. - # - target_dataset = self.get_dataset( trans, target_dataset_id, check_ownership=False, check_accessible=True ) - if target_dataset.history.user == trans.user: - target_history = target_dataset.history - else: - target_history = trans.get_history( create=True ) - - # HACK: tools require unencoded parameters but kwargs are typically - # encoded, so try decoding all parameter values. - for key, value in kwargs.items(): - try: - value = trans.security.decode_id( value ) - kwargs[ key ] = value - except: - pass - - # - # Execute tool. - # - tool = trans.app.toolbox.get_tool( tool_id ) - if not tool: - return trans.app.model.Dataset.conversion_messages.NO_TOOL - - # HACK: add run button so that tool.handle_input will run tool. - kwargs['runtool_btn'] = 'Execute' - params = util.Params( kwargs, sanitize=False ) - template, vars = tool.handle_input( trans, params.__dict__, history=target_history ) - - # TODO: check for errors and ensure that output dataset is available. - output_datasets = vars[ 'out_data' ].values() - return self.add_track_async( trans, output_datasets[0].id ) - def _rerun_tool( self, trans, payload, **kwargs ): """ Rerun a tool to produce a new output dataset that corresponds to a @@ -318,7 +276,7 @@ else: # Recursive search. return_val = False - for name, value in param_dict.items(): + for value in param_dict.values(): if isinstance( value, dict ): return_val = set_value( value, group_name, group_index, param_name, param_value) if return_val: https://bitbucket.org/galaxy/galaxy-central/commits/f5901304ca0f/ Changeset: f5901304ca0f User: nsoranzo Date: 2014-04-10 18:35:18 Summary: Remove unused method. Cleanup imports. Affected #: 1 file diff -r be7d6bac2fb115bad61d92db0efeef24deafc73a -r f5901304ca0f5aaeb1c745fad0b2e1990246701c lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,12 +1,9 @@ """ API operations on the contents of a folder. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * +import logging +from galaxy import web +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems log = logging.getLogger( __name__ ) @@ -70,8 +67,7 @@ trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) - path_to_root = [] - def build_path ( folder ): + def build_path( folder ): """ Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. """ @@ -148,12 +144,3 @@ PUT /api/folders/{encoded_folder_id}/contents """ pass - - # TODO: Move to library_common. - def __decode_library_content_id( self, trans, content_id ): - if ( len( content_id ) % 16 == 0 ): - return 'LibraryDataset', content_id - elif ( content_id.startswith( 'F' ) ): - return 'LibraryFolder', content_id[1:] - else: - raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) https://bitbucket.org/galaxy/galaxy-central/commits/2d94528383ff/ Changeset: 2d94528383ff User: nsoranzo Date: 2014-04-10 19:56:43 Summary: PEP8 whitespace fixes. Affected #: 1 file diff -r f5901304ca0f5aaeb1c745fad0b2e1990246701c -r 2d94528383ff8115a0fa54ba48b395e5d9f2b3ed lib/galaxy/webapps/galaxy/api/group_users.py --- a/lib/galaxy/webapps/galaxy/api/group_users.py +++ b/lib/galaxy/webapps/galaxy/api/group_users.py @@ -58,7 +58,7 @@ email = user.email, url = url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This if not item: - item = "user %s not in group %s" % (user.email,group.name) + item = "user %s not in group %s" % (user.email, group.name) except Exception, e: item = "Error in group_user API group %s user %s" % (group.name, user.email) log.error(item + ": %s" % str(e)) @@ -92,7 +92,7 @@ email = user.email, url = url_for( 'group_user', group_id=group_id, id=user_id) ) except Exception, e: - item = "Error in group_user API Adding user %s to group %s" % (user.email,group.name) + item = "Error in group_user API Adding user %s to group %s" % (user.email, group.name) log.error(item + ": %s" % str(e)) return item @@ -117,8 +117,8 @@ email = user.email, url = url_for( 'group_user', group_id=group_id, id=user_id) ) if not item: - item = "user %s not in group %s" % (user.email,group.name) + item = "user %s not in group %s" % (user.email, group.name) except Exception, e: - item = "Error in group_user API Removing user %s from group %s" % (user.email,group.name) + item = "Error in group_user API Removing user %s from group %s" % (user.email, group.name) log.error(item + ": %s" % str(e)) return item https://bitbucket.org/galaxy/galaxy-central/commits/e27648dda033/ Changeset: e27648dda033 User: nsoranzo Date: 2014-04-10 19:57:25 Summary: Fix a broken import. Cleanup imports. Affected #: 4 files diff -r 2d94528383ff8115a0fa54ba48b395e5d9f2b3ed -r e27648dda033d38c8db07d1353ad1193411d2751 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -1,7 +1,7 @@ -from galaxy import config, tools, web, util -from galaxy.web.base.controller import BaseController, BaseAPIController -from galaxy.util.bunch import Bunch +from galaxy import web, util +from galaxy.web.base.controller import BaseAPIController from galaxy.web.framework.helpers import is_true +from galaxy.webapps.galaxy.controllers.data_admin import build_param_dict as massage def get_id( base, format ): if format: @@ -76,7 +76,6 @@ # 'download' Download and index # 'index' Index only params = util.Params( payload ) - from galaxy.web.controllers.data_admin import build_param_dict as massage paramdict = massage( params, trans ) func = params.get( 'func', 'download' ) if func == 'download': diff -r 2d94528383ff8115a0fa54ba48b395e5d9f2b3ed -r e27648dda033d38c8db07d1353ad1193411d2751 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -8,7 +8,6 @@ pkg_resources.require( "Paste" ) from galaxy import exceptions -from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web import _future_expose_api_raw as expose_api_raw diff -r 2d94528383ff8115a0fa54ba48b395e5d9f2b3ed -r e27648dda033d38c8db07d1353ad1193411d2751 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -4,7 +4,6 @@ from galaxy import exceptions from galaxy import util -from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous @@ -18,7 +17,6 @@ from galaxy.web.base.controller import UsesTagsMixin from galaxy.web.base.controller import url_for -from galaxy.util.sanitize_html import sanitize_html from galaxy.webapps.galaxy.api import histories diff -r 2d94528383ff8115a0fa54ba48b395e5d9f2b3ed -r e27648dda033d38c8db07d1353ad1193411d2751 lib/galaxy/webapps/galaxy/api/metrics.py --- a/lib/galaxy/webapps/galaxy/api/metrics.py +++ b/lib/galaxy/webapps/galaxy/api/metrics.py @@ -7,7 +7,6 @@ import datetime from galaxy import exceptions -from galaxy import web from galaxy.web import require_admin from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous https://bitbucket.org/galaxy/galaxy-central/commits/6e2eaa8626b2/ Changeset: 6e2eaa8626b2 User: nsoranzo Date: 2014-04-10 20:00:45 Summary: Fix old wiki links. Affected #: 14 files diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -3,7 +3,7 @@ ; ; This file is version controlled and should not be edited by hand! ; For more information, see: -; http://wiki.g2.bx.psu.edu/Admin/Config/Eggs +; https://wiki.galaxyproject.org/Admin/Config/Eggs ; [general] diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -217,7 +217,7 @@ self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) + self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -50,7 +50,7 @@ self.smtp_server = kwargs.get( 'smtp_server', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -941,7 +941,7 @@ message += 'attribute value which is a directory relative to the Galaxy installation directory in order ' message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> ' message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' - message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation ' + message += '<a href="https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy" target="_blank">Installation ' message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool ' message += 'Shed wiki for all of the details.' return trans.show_error_message( message ) diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -39,7 +39,7 @@ self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -96,8 +96,8 @@ self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) + self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.biostar_url = kwargs.get( 'biostar_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 scripts/dist-scramble.py --- a/scripts/dist-scramble.py +++ b/scripts/dist-scramble.py @@ -1,7 +1,7 @@ """ Scrambles eggs for distribution on multiple platforms. -(from http://wiki.g2.bx.psu.edu/Admin/Config/Eggs) +(from https://wiki.galaxyproject.org/Admin/Config/Eggs ) This is mostly designed for use by Galaxy Developers at Penn State who are building eggs for distribution via the Galaxy Eggs distribution site. dist-scramble.py uses the dist-eggs.ini config file to determine what platforms diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 static/scripts/viz/phyloviz.js --- a/static/scripts/viz/phyloviz.js +++ b/static/scripts/viz/phyloviz.js @@ -737,7 +737,7 @@ $("#nodeSelectionView").show(); } }, { icon_class: 'information', title: 'Phyloviz Help', on_click: function() { - window.open('http://wiki.g2.bx.psu.edu/Learn/Visualization/PhylogeneticTree'); + window.open('https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree'); // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrC… } } ], diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -50,11 +50,11 @@ repository tools may include code that produces malicious behavior, so be aware of what you are installing. </p><p> - If you discover a repository that causes problems after installation, contact <a href="http://wiki.g2.bx.psu.edu/Support" target="_blank">Galaxy support</a>, + If you discover a repository that causes problems after installation, contact <a href="https://wiki.galaxyproject.org/Support" target="_blank">Galaxy support</a>, sending all necessary information, and appropriate action will be taken. </p><p> - <a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Contacting_the_owner_of_a_repository" target="_blank">Contact the repository owner</a> for + <a href="https://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contact_repositor…" target="_blank">Contact the repository owner</a> for general questions or concerns. </p></div> diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -50,11 +50,11 @@ repository tools may include code that produces malicious behavior, so be aware of what you are installing. </p><p> - If you discover a repository that causes problems after installation, contact <a href="http://wiki.g2.bx.psu.edu/Support" target="_blank">Galaxy support</a>, + If you discover a repository that causes problems after installation, contact <a href="https://wiki.galaxyproject.org/Support" target="_blank">Galaxy support</a>, sending all necessary information, and appropriate action will be taken. </p><p> - <a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Contacting_the_owner_of_a_repository" target="_blank">Contact the repository owner</a> for + <a href="https://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contact_repositor…" target="_blank">Contact the repository owner</a> for general questions or concerns. </p></div> diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -37,7 +37,7 @@ %if trans.app.config.enable_quotas: Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>. %endif - Is your usage more than expected? See the <a href="http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets" target="_blank">documentation</a> for tips on how to find all of the data in your account. + Is your usage more than expected? See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account. </p> %endif %else: diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 tool_shed_wsgi.ini.sample --- a/tool_shed_wsgi.ini.sample +++ b/tool_shed_wsgi.ini.sample @@ -55,7 +55,7 @@ # User authentication can be delegated to an upstream proxy server (usually # Apache). The upstream proxy should set a REMOTE_USER header in the request. # Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy #use_remote_user = False # Configuration for debugging middleware @@ -82,7 +82,7 @@ #email_from = your_tool_shed_email@server # The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.g2.bx.psu.edu/Support +#support_url = https://wiki.galaxyproject.org/Support # Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) ## use_heartbeat = True diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 tools/data_source/microbial_import.xml --- a/tools/data_source/microbial_import.xml +++ b/tools/data_source/microbial_import.xml @@ -109,7 +109,6 @@ **Note:** Having trouble locating your organism? Click here_ for a list of available species and their location. -.. _here: http://wiki.g2.bx.psu.edu/Main/Data%20Libraries/Microbes - +.. _here: https://wiki.galaxyproject.org/Main/Data%20Libraries/Microbes </help></tool> diff -r e27648dda033d38c8db07d1353ad1193411d2751 -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 tools/next_gen_conversion/fastq_gen_conv.xml --- a/tools/next_gen_conversion/fastq_gen_conv.xml +++ b/tools/next_gen_conversion/fastq_gen_conv.xml @@ -75,7 +75,7 @@ A good description of fastq datasets can be found `here`__, while a description of Galaxy's fastq "logic" can be found `here`__. Because ranges of quality values within different types of fastq datasets overlap it very difficult to detect them automatically. This tool supports conversion of two commonly found types (Solexa/Illumina 1.0 and Illumina 1.3+) into fastq Sanger. .. __: http://en.wikipedia.org/wiki/FASTQ_format - .. __: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup + .. __: https://wiki.galaxyproject.org/Learn/Datatypes#Fastq .. class:: warningmark https://bitbucket.org/galaxy/galaxy-central/commits/2c6c7971d666/ Changeset: 2c6c7971d666 User: nsoranzo Date: 2014-04-11 12:00:39 Summary: Merge galaxy/galaxy-central default branch. Affected #: 77 files diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -60,6 +60,10 @@ status_code = 400 err_code = error_codes.MALFORMED_ID +class UnknownContentsType( MessageException ): + status_code = 400 + err_code = error_codes.UNKNOWN_CONTENTS_TYPE + class RequestParameterMissingException( MessageException ): status_code = 400 err_code = error_codes.USER_REQUEST_MISSING_PARAMETER diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -50,6 +50,11 @@ "message": "The id of the resource is malformed." }, { + "name": "UNKNOWN_CONTENTS_TYPE", + "code": 400010, + "message": "The request contains unknown type of contents." + }, + { "name": "USER_NO_API_KEY", "code": 403001, "message": "API authentication required for this request" diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,6 +4,7 @@ from galaxy.util.bunch import Bunch from galaxy.util import asbool from tool_shed.util import common_util +from urlparse import urljoin log = logging.getLogger( __name__ ) @@ -73,6 +74,12 @@ def can_reinstall_or_activate( self ): return self.deleted + def get_sharable_url( self, app ): + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed ) + if tool_shed_url: + return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) + return tool_shed_url + def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -28,7 +28,9 @@ ----------------------------------------------------------------------------- job id: ${job_id} tool id: ${job_tool_id} +tool version: ${tool_version} job pid or drm id: ${job_runner_external_id} +job tool version: ${job_tool_version} ----------------------------------------------------------------------------- job command line: ${job_command_line} @@ -86,7 +88,9 @@ history_item_name=hda.get_display_name(), history_view_link=history_view_link, job_id=job.id, + tool_version=job.tool_version, job_tool_id=job.tool_id, + job_tool_version=hda.tool_version, job_runner_external_id=job.job_runner_external_id, job_command_line=job.command_line, job_stderr=util.unicodify( job.stderr ), diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -979,7 +979,7 @@ if option[2]: # Found selected option. value = option[1] - d[ 'value' ] = options + d[ 'value' ] = value return d diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -86,7 +86,14 @@ def populate_tool_payload( payload=None, tool=None ): payload = populate_tag_payload( payload=payload, tool=tool ) payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) - payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ) + tool_url = None + if tool.tool_shed_repository: + tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + if tool_url: + tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url ) + if not tool_url: + tool_url = '' + payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url ) return payload def determine_cookie_domain( galaxy_hostname, biostar_hostname ): diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,10 +1,15 @@ """ -API operations on the contents of a folder. +API operations on the contents of a library folder. """ -import logging from galaxy import web +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems +import logging log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @@ -12,7 +17,111 @@ Class controls retrieval, creation and updating of folder contents. """ - def load_folder_contents( self, trans, folder ): + @expose_api_anonymous + def index( self, trans, folder_id, **kwd ): + """ + GET /api/folders/{encoded_folder_id}/contents + Displays a collection (list) of a folder's contents (files and folders). + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided in response as a separate object providing data for breadcrumb path building. + """ + + if ( len( folder_id ) == 17 and folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[ 1: ] ) + except TypeError: + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) ) + else: + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) ) + + try: + folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple folders with same id found.' ) + except NoResultFound: + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + except Exception: + raise exceptions.InternalServerError( 'Error loading from the database.' ) + + current_user_roles = trans.get_current_user_roles() + can_add_library_item = trans.user_is_admin() or trans.app.security_agent.can_add_library_item( current_user_roles, folder ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + if folder.parent_id == None: + try: + library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one() + except Exception: + raise exceptions.InternalServerError( 'Error loading from the database.' ) + if trans.app.security_agent.library_is_public( library, contents=False ): + pass + else: + if trans.user: + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + else: + log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + else: + if trans.user: + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + else: + log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + + def build_path( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb building purposes. + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) + return path_to_root + + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] + + folder_contents = [] + time_updated = '' + time_created = '' + # Go through every accessible item in the folder and include its meta-data. + for content_item in self._load_folder_contents( trans, folder ): + if trans.app.security_agent.can_access_library_item( current_user_roles, content_item, trans.user ): + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id + return_item.update ( dict ( item_count = content_item.item_count ) ) + + if content_item.api_type == 'file': + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) + + return { 'metadata' : { 'full_path' : full_path, 'can_add_library_item': can_add_library_item }, 'folder_contents' : folder_contents } + + def _load_folder_contents( self, trans, folder ): """ Loads all contents of the folder (folders and data sets) but only in the first level. """ @@ -34,100 +143,11 @@ return content_items @web.expose_api - def index( self, trans, folder_id, **kwd ): - """ - GET /api/folders/{encoded_folder_id}/contents - Displays a collection (list) of a folder's contents (files and folders). - Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. - Full path is provided as a separate object in response providing data for breadcrumb path building. - """ - folder_container = [] - current_user_roles = trans.get_current_user_roles() - - if ( folder_id.startswith( 'F' ) ): - try: - decoded_folder_id = trans.security.decode_id( folder_id[1:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) - - try: - folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - except: - folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - - # We didn't find the folder or user does not have an access to it. - if not folder: - trans.response.status = 400 - return "Invalid folder id ( %s ) specified." % str( folder_id ) - - if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): - log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) - trans.response.status = 400 - return "Invalid folder id ( %s ) specified." % str( folder_id ) - - def build_path( folder ): - """ - Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. - """ - path_to_root = [] - # We are almost in root - if folder.parent_id is None: - path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) - else: - # We add the current folder and traverse up one folder. - path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) - upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) - path_to_root.extend( build_path( upper_folder ) ) - return path_to_root - - # Return the reversed path so it starts with the library node. - full_path = build_path( folder )[::-1] - folder_container.append( dict( full_path = full_path ) ) - - folder_contents = [] - time_updated = '' - time_created = '' - # Go through every item in the folder and include its meta-data. - for content_item in self.load_folder_contents( trans, folder ): - return_item = {} - encoded_id = trans.security.encode_id( content_item.id ) - time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) - time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) - - # For folder return also hierarchy values - if content_item.api_type == 'folder': - encoded_id = 'F' + encoded_id - return_item.update ( dict ( item_count = content_item.item_count ) ) - - if content_item.api_type == 'file': - library_dataset_dict = content_item.to_dict() - library_dataset_dict['data_type'] - library_dataset_dict['file_size'] - library_dataset_dict['date_uploaded'] - return_item.update ( dict ( data_type = library_dataset_dict['data_type'], - file_size = library_dataset_dict['file_size'], - date_uploaded = library_dataset_dict['date_uploaded'] ) ) - - # For every item return also the default meta-data - return_item.update( dict( id = encoded_id, - type = content_item.api_type, - name = content_item.name, - time_updated = time_updated, - time_created = time_created - ) ) - folder_contents.append( return_item ) - # Put the data in the container - folder_container.append( dict( folder_contents = folder_contents ) ) - return folder_container - - @web.expose_api def show( self, trans, id, library_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/ """ - pass + raise exceptions.NotImplemented( 'Showing the library folder content is not implemented.' ) @web.expose_api def create( self, trans, library_id, payload, **kwd ): @@ -136,11 +156,11 @@ Creates a new folder. This should be superseded by the LibraryController. """ - pass + raise exceptions.NotImplemented( 'Creating the library folder content is not implemented.' ) @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/folders/{encoded_folder_id}/contents """ - pass + raise exceptions.NotImplemented( 'Updating the library folder content is not implemented.' ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -1,14 +1,17 @@ """ -API operations on folders +API operations on library folders """ -import logging, os, string, shutil, urllib, re, socket, traceback +import os, string, shutil, urllib, re, socket, traceback from galaxy import datatypes, jobs, web, security +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web.base.controller import BaseAPIController,UsesLibraryMixin,UsesLibraryMixinItems from galaxy.util.sanitize_html import sanitize_html from cgi import escape, FieldStorage from paste.httpexceptions import HTTPBadRequest +import logging log = logging.getLogger( __name__ ) class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @@ -18,9 +21,9 @@ """ GET /api/folders/ This would normally display a list of folders. However, that would - be across multiple libraries, so it's not implemented yet. + be across multiple libraries, so it's not implemented. """ - pass + raise exceptions.NotImplemented( 'Listing all accessible library folders is not implemented.' ) @web.expose_api def show( self, trans, id, **kwd ): diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -188,8 +188,7 @@ hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) return hda_dict - #TODO: allow anon users to copy hdas, ldas - @expose_api + @expose_api_anonymous def create( self, trans, history_id, payload, **kwd ): """ create( self, trans, history_id, payload, **kwd ) @@ -434,10 +433,7 @@ return validated_payload def __handle_unknown_contents_type( self, trans, contents_type ): - # TODO: raise a message exception instead of setting status and returning dict. - trans.response.status = 400 - return { 'error': 'Unknown contents type %s' % type } - + raise exceptions.UnknownContentsType('Unknown contents type: %s' % type) class HDAManager( object ): diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 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 @@ -12,9 +12,13 @@ import urllib import urllib2 import zipfile -from paste.httpexceptions import HTTPBadRequest -from galaxy import util, web -from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +# from paste.httpexceptions import HTTPBadRequest +from galaxy import util +from galaxy import web +# from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound from galaxy.security import Action from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin @@ -24,7 +28,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): - @web.expose_api + @expose_api_anonymous def show( self, trans, id, **kwd ): """ show( self, trans, id, **kwd ) @@ -41,19 +45,20 @@ try: dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) except Exception, e: - trans.response.status = 500 - return str( e ) - try: - rval = dataset.to_dict() - except Exception, e: - rval = "Error in dataset API at listing contents: " + str( e ) - log.error( rval + ": %s" % str(e), exc_info=True ) - trans.response.status = 500 - return "Error in dataset API at listing contents: " + str( e ) + raise exceptions.ObjectNotFound( 'Requested dataset was not found.' ) + # trans.response.status = 500 + # return str( e ) + # try: + rval = dataset.to_dict() + # except Exception, e: + # rval = "Error in dataset API at listing contents: " + str( e ) + # log.error( rval + ": %s" % str(e), exc_info=True ) + # trans.response.status = 500 + # return "Error in dataset API at listing contents: " + str( e ) rval['id'] = trans.security.encode_id(rval['id']); rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); - rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id']) return rval @web.expose diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -7,7 +7,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.model.orm import and_, not_, or_ -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import BaseAPIController import logging log = logging.getLogger( __name__ ) @@ -61,7 +61,6 @@ if trans.app.security_agent.library_is_public( library, contents=False ): item[ 'public' ] = True current_user_roles = trans.get_current_user_roles() - # can_user_add = trans.app.security_agent.can_add_library_item( current_user_roles, library.root_folder ) if not trans.user_is_admin(): item['can_user_add'] = trans.app.security_agent.can_add_library_item( current_user_roles, library ) item['can_user_modify'] = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) @@ -98,7 +97,7 @@ deleted = util.string_as_bool( deleted ) try: decoded_library_id = trans.security.decode_id( library_id ) - except Exception: + except TypeError: raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id ) try: library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) @@ -144,7 +143,14 @@ library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() - return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + + item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + item['can_user_add'] = True + item['can_user_modify'] = True + item['can_user_manage'] = True + if trans.app.security_agent.library_is_public( library, contents=False ): + item[ 'public' ] = True + return item @expose_api def update( self, trans, id, **kwd ): diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -17,8 +17,7 @@ log = logging.getLogger( __name__ ) -class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, - UsesHistoryDatasetAssociationMixin ): +class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ): @expose_api def index( self, trans, library_id, **kwd ): diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -284,7 +284,7 @@ # ==================== # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + webapp.add_route( '/admin_toolshed/static/images/:repository_id/{image_file:.+?}', controller='admin_toolshed', action='display_image_in_repository', repository_id=None, diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -16,6 +16,7 @@ from tool_shed.util import data_manager_util from tool_shed.util import datatype_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util @@ -1851,7 +1852,7 @@ repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) ) else: repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) - repo = hg.repository( suc.get_configured_ui(), path=repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), path=repo_files_dir ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) suc.update_repository( repo, latest_ctx_rev ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -13,6 +13,7 @@ import tool_shed.util.shed_util_common as suc from tool_shed.galaxy_install import repository_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util @@ -49,7 +50,7 @@ log.debug( error_message ) return [] repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) return ordered_installable_revisions else: @@ -133,7 +134,7 @@ # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -6,6 +6,7 @@ from galaxy.model.orm import and_, not_, select from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest from tool_shed.util import export_util +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc from galaxy import eggs @@ -168,7 +169,7 @@ # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository_dependency.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency, repo, changeset_revision ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -19,6 +19,7 @@ from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import export_util +from tool_shed.util import hg_util from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import readme_util @@ -719,7 +720,7 @@ status = kwd.get( 'status', 'done' ) commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. suc.update_repository( repo ) changeset_revision = repository.tip( trans.app ) @@ -891,9 +892,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Default to the current changeset revision. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) latest_changeset_revision = changeset_revision from_update_manager = kwd.get( 'from_update_manager', False ) if from_update_manager: @@ -937,10 +938,10 @@ update_to_changeset_hash = None for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: if changeset_hash == repository.tip( trans.app ): - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash break else: @@ -949,7 +950,7 @@ changeset_hash ) if repository_metadata: # We found a RepositoryMetadata record. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash break else: @@ -1213,7 +1214,7 @@ else: containers_dict = None export_repository_dependencies_check_box = None - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return trans.fill_template( "/webapps/tool_shed/repository/export_repository.mako", changeset_revision=changeset_revision, containers_dict=containers_dict, @@ -1466,9 +1467,9 @@ has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ] repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) ctx_rev = str( update_to_ctx.rev() ) latest_changeset_revision = changeset_revision update_dict = dict( changeset_revision=changeset_revision, @@ -1497,7 +1498,7 @@ has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False changeset_hash = str( repo.changectx( changeset ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), @@ -1515,10 +1516,10 @@ # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash else: - update_to_ctx = suc.get_changectx_for_changeset( repo, update_to_changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, update_to_changeset_hash ) latest_changeset_revision = update_to_changeset_hash break elif not update_to_changeset_hash and changeset_hash == changeset_revision: @@ -1544,8 +1545,8 @@ changeset_revision = kwd[ 'changeset_revision' ] repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) if ctx: return str( ctx.rev() ) return '' @@ -1560,8 +1561,8 @@ def get_file_from_changeset_revision( self, repo_files_dir, changeset_revision, file_name, dir ): """Return file_name from the received changeset_revision of the repository manifest.""" stripped_file_name = suc.strip_path( file_name ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir ) return named_tmp_file @@ -1604,7 +1605,7 @@ trans.model.Repository.table.c.user_id == user.id ) ): repository = repository_metadata.repository repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) latest_downloadable_changeset_revsion = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) if repository_metadata.changeset_revision == latest_downloadable_changeset_revsion: # We'll display only the test run for the latest installable revision in the rss feed. @@ -1672,7 +1673,7 @@ if repository_name is not None and repository_owner is not None: repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) if repository: - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) return suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) return suc.INITIAL_CHANGELOG_HASH @@ -1855,7 +1856,7 @@ changeset_revision = kwd[ 'changeset_revision' ] repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) tool_version_dicts = [] for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) @@ -1880,7 +1881,7 @@ repository_id = trans.security.encode_id( repository.id ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if not repository_metadata: # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository @@ -1889,7 +1890,7 @@ repo, after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = repository_util.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, @@ -2165,7 +2166,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) repository_type = kwd.get( 'repository_type', str( repository.type ) ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repo_name = kwd.get( 'repo_name', repository.name ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) description = kwd.get( 'description', repository.description ) @@ -2317,7 +2318,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False ) repository_metadata = None metadata = None is_malicious = False @@ -2326,7 +2327,7 @@ if changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious else: @@ -2337,7 +2338,7 @@ if previous_changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision ) if repository_metadata: - revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious changeset_revision = previous_changeset_revision @@ -2443,7 +2444,7 @@ # There is no repository_metadata defined for the changeset_revision, so see if it was defined # in a previous changeset in the changelog. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) previous_changeset_revision = \ suc.get_previous_metadata_changeset_revision( repository, repo, @@ -2520,7 +2521,7 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the next installable changeset_revision beyond the received changeset_revision. changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if changeset_revision: @@ -2540,7 +2541,7 @@ status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: @@ -2577,7 +2578,7 @@ repository_metadata_id = None metadata = None repository_dependencies = None - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, @@ -2607,7 +2608,7 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the lower bound changeset revision. lower_bound_changeset_revision = suc.get_previous_metadata_changeset_revision( repository, repo, changeset_revision, downloadable=True ) # Build the list of changeset revision hashes. @@ -2633,7 +2634,7 @@ status='error' ) ) repository = suc.get_repository_in_tool_shed( trans, id ) changeset_revision = repository.tip( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -2651,7 +2652,7 @@ changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, @@ -2702,7 +2703,7 @@ commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' ) if kwd.get( 'select_files_to_delete_button', False ): if selected_files_to_delete: @@ -2742,7 +2743,7 @@ # Update the repository files for browsing. suc.update_repository( repo ) # Get the new repository tip. - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) if tip == repository.tip( trans.app ): message += 'No changes to repository. ' kwd[ 'message' ] = message @@ -2931,7 +2932,7 @@ if not repository_metadata: # Get updates to the received changeset_revision if any exist. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if upper_bound_changeset_revision: changeset_revision = upper_bound_changeset_revision @@ -2971,7 +2972,7 @@ trans.security.encode_id( repository.id ), changeset_revision ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) tool_shed_status_dict = {} # Handle repository deprecation. tool_shed_status_dict[ 'repository_deprecated' ] = str( repository.deprecated ) @@ -3063,7 +3064,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) changesets = [] for changeset in repo.changelog: ctx = repo.changectx( changeset ) @@ -3074,7 +3075,7 @@ change_dict = { 'ctx' : ctx, 'rev' : str( ctx.rev() ), 'date' : date, - 'display_date' : suc.get_readable_ctx_date( ctx ), + 'display_date' : hg_util.get_readable_ctx_date( ctx ), 'description' : ctx.description(), 'files' : ctx.files(), 'user' : ctx.user(), @@ -3098,8 +3099,8 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, ctx_str ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = hg_util.get_changectx_for_changeset( repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' @@ -3129,7 +3130,7 @@ metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: - ctx_parent_date = suc.get_readable_ctx_date( ctx_parent ) + ctx_parent_date = hg_util.get_readable_ctx_date( ctx_parent ) ctx_parent_rev = ctx_parent.rev() if ctx_parent_rev < 0: prev = None @@ -3138,7 +3139,7 @@ else: prev = None if ctx_child: - ctx_child_date = suc.get_readable_ctx_date( ctx_child ) + ctx_child_date = hg_util.get_readable_ctx_date( ctx_child ) ctx_child_rev = ctx_child.rev() next = "<b>%s:%s</b><i>(%s)</i>" % ( ctx_child_rev, ctx_child, ctx_child_date ) else: @@ -3187,7 +3188,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) display_reviews = kwd.get( 'display_reviews', False ) @@ -3221,7 +3222,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -3277,13 +3278,13 @@ render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) tool_metadata_dict = {} tool_lineage = [] tool = None guid = None original_tool_data_path = trans.app.config.tool_data_path - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -7,6 +7,7 @@ from galaxy.webapps.tool_shed.util import ratings_util from tool_shed.util.container_util import STRSEP import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import review_util from galaxy.util.odict import odict import tool_shed.grids.repository_review_grids as repository_review_grids @@ -72,8 +73,8 @@ status = kwd.get( 'status', 'done' ) review = review_util.get_review( trans, kwd[ 'id' ] ) repository = review.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako', repository=repository, changeset_revision_label=changeset_revision_label, @@ -232,7 +233,7 @@ for component in review_util.get_components( trans ): components_dict[ component.name ] = dict( component=component, component_review=None ) repository = review.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) for component_review in review.component_reviews: if component_review and component_review.component: component_name = component_review.component.name @@ -337,7 +338,7 @@ name='revision_approved', selected_value=selected_value, for_component=False ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako', repository=repository, review=review, @@ -470,7 +471,7 @@ if repository_id: repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] reviews_dict = odict() @@ -478,7 +479,7 @@ ctx = repo.changectx( changeset ) changeset_revision = str( ctx ) if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes: - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) if changeset_revision in reviewed_revision_hashes: # Find the review for this changeset_revision repository_reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) @@ -517,9 +518,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako', repository=repository, @@ -582,9 +583,9 @@ status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) previous_reviews_dict = review_util.get_previous_repository_reviews( trans, repository, changeset_revision ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako', repository=repository, changeset_revision=changeset_revision, diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -11,6 +11,7 @@ import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc from tool_shed.util import commit_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_dependency_util from tool_shed.util import tool_dependency_util @@ -39,7 +40,7 @@ repository_id = kwd.get( 'repository_id', '' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) ) remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None @@ -63,7 +64,7 @@ repo_url = 'http%s' % url[ len( 'hg' ): ] repo_url = repo_url.encode( 'ascii', 'replace' ) try: - commands.clone( suc.get_configured_ui(), repo_url, uploaded_directory ) + commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory ) except Exception, e: message = 'Error uploading via mercurial clone: %s' % suc.to_html_string( str( e ) ) status = 'error' @@ -323,7 +324,7 @@ def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 if upload_point is not None: @@ -387,7 +388,7 @@ def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 ok, message = commit_util.check_archive( repository, tar ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -15,6 +15,7 @@ from tool_shed.util import data_manager_util from tool_shed.util import datatype_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import repository_dependency_util from tool_shed.util import metadata_util from tool_shed.util import tool_dependency_util @@ -186,7 +187,7 @@ def get_repo_info_dict( trans, repository_id, changeset_revision ): repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, @@ -225,7 +226,7 @@ has_repository_dependencies_only_if_compiling_contained_td = False includes_tool_dependencies = False includes_tools_for_display_in_tool_panel = False - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, @@ -574,7 +575,7 @@ current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_ctx_rev != ctx_rev: - repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) + repo = hg.repository( hg_util.get_configured_ui(), path=os.path.abspath( install_dir ) ) pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) handle_repository_contents( trans, @@ -804,7 +805,7 @@ def pull_repository( repo, repository_clone_url, ctx_rev ): """Pull changes from a remote repository to a local one.""" - commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) + commands.pull( hg_util.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) def repair_tool_shed_repository( trans, repository, repo_info_dict ): diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -5,6 +5,7 @@ from galaxy.webapps.tool_shed import model from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.grids.repository_grids import CategoryGrid from tool_shed.grids.repository_grids import RepositoryGrid @@ -425,9 +426,11 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - return suc.get_revision_label( trans, repository, repository_metadata.changeset_revision, include_date=True ) + return hg_util.get_revision_label( trans, + repository, + repository_metadata.changeset_revision, + include_date=True, + include_hash=True ) class ToolsColumn( grids.TextColumn ): diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -6,6 +6,7 @@ from galaxy.model.orm import or_ from galaxy.util import json from galaxy.util import listify +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc import tool_shed.grids.util as grids_util import tool_shed.repository_types.util as rt_util @@ -116,7 +117,7 @@ def get_value( self, trans, grid, repository ): """Display the current repository heads.""" repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) heads = suc.get_repository_heads( repo ) multiple_heads = len( heads ) > 1 if multiple_heads: @@ -124,7 +125,7 @@ else: heads_str = '' for ctx in heads: - heads_str += '%s<br/>' % suc.get_revision_label_from_ctx( ctx, include_date=True ) + heads_str += '%s<br/>' % hg_util.get_revision_label_from_ctx( ctx, include_date=True ) heads_str.rstrip( '<br/>' ) if multiple_heads: heads_str += '</font>' @@ -1338,7 +1339,7 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository changeset_revision = repository_metadata.changeset_revision - changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + changeset_revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return changeset_revision_label @@ -1482,7 +1483,7 @@ changeset_revision ) if not required_repository_metadata: repo_dir = required_repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) updated_changeset_revision = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset_revision ) required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, @@ -2029,7 +2030,7 @@ tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) repository_metadata = None try: @@ -2077,7 +2078,7 @@ tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) try: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -6,6 +6,7 @@ from galaxy.model.orm import or_ from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import metadata_util from galaxy import eggs @@ -66,10 +67,10 @@ # Restrict to revisions that have been reviewed. if repository.reviews: rval = '' - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) for review in repository.reviews: changeset_revision = review.changeset_revision - rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \ ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval @@ -85,9 +86,11 @@ rval = '' for repository_metadata in repository_metadata_revisions: rev, label, changeset_revision = \ - metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository, + include_date=True, + include_hash=False ) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \ ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval @@ -308,7 +311,11 @@ rval += 'edit_review' else: rval +='browse_review' - revision_label = suc.get_revision_label( trans, review.repository, review.changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, + review.repository, + review.changeset_revision, + include_date=True, + include_hash=False ) rval += '?id=%s">%s</a>' % ( encoded_review_id, revision_label ) return rval diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -1,7 +1,7 @@ import logging import os import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util +from tool_shed.util import hg_util from galaxy.web.form_builder import SelectField from galaxy.util.bunch import Bunch @@ -96,9 +96,11 @@ repository_metadata_revisions = repository.metadata_revisions for repository_metadata in repository_metadata_revisions: rev, label, changeset_revision = \ - metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository, + include_date=True, + include_hash=False ) changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -14,6 +14,7 @@ import ConfigParser import galaxy.webapps.tool_shed.config as tool_shed_config +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc import logging import shutil @@ -109,7 +110,7 @@ if tool_dicts is not None: # Clone the repository up to the changeset revision we're checking. repo_dir = repository.repo_path( app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cafr" ) cloned_ok, error_message = suc.clone_repository( repo_dir, work_dir, changeset_revision ) if cloned_ok: @@ -368,7 +369,7 @@ """ if not testable_revision: repo_dir = repository.repo_path( app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) if len( changeset_revisions ) > 1: latest_downloadable_revision = changeset_revisions[ -1 ] diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -12,6 +12,7 @@ from galaxy.util.odict import odict from galaxy.web import url_for import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import tool_util from tool_shed.util import xml_util import tool_shed.repository_types.util as rt_util @@ -156,7 +157,7 @@ def handle_directory_changes( trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) content_alert_str = '' files_to_remove = [] filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ] @@ -342,7 +343,7 @@ repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if repository: repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) lastest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) if lastest_installable_changeset_revision != suc.INITIAL_CHANGELOG_HASH: elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -14,6 +14,7 @@ from tool_shed.util import common_install_util from tool_shed.util import common_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import repository_dependency_util from tool_shed.util import xml_util @@ -37,7 +38,7 @@ def archive_repository_revision( trans, ui, repository, archive_dir, changeset_revision ): '''Create an un-versioned archive of a repository.''' - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) options_dict = suc.get_mercurial_default_options_dict( 'archive' ) options_dict[ 'rev' ] = changeset_revision error_message = '' @@ -233,8 +234,8 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = {} # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/hg_util.py --- /dev/null +++ b/lib/tool_shed/util/hg_util.py @@ -0,0 +1,108 @@ +import logging +from datetime import datetime +from time import gmtime +from time import strftime + +from galaxy import eggs +eggs.require( 'mercurial' ) + +from mercurial import cmdutil +from mercurial import commands +from mercurial import hg +from mercurial import ui + +def get_changectx_for_changeset( repo, changeset_revision, **kwd ): + """Retrieve a specified changectx from a repository.""" + for changeset in repo.changelog: + ctx = repo.changectx( changeset ) + if str( ctx ) == changeset_revision: + return ctx + return None + +def get_configured_ui(): + """Configure any desired ui settings.""" + _ui = ui.ui() + # The following will suppress all messages. This is + # the same as adding the following setting to the repo + # hgrc file' [ui] section: + # quiet = True + _ui.setconfig( 'ui', 'quiet', True ) + return _ui + +def get_readable_ctx_date( ctx ): + """Convert the date of the changeset (the received ctx) to a human-readable date.""" + t, tz = ctx.date() + date = datetime( *gmtime( float( t ) - tz )[ :6 ] ) + ctx_date = date.strftime( "%Y-%m-%d" ) + return ctx_date + +def get_revision_label( trans, repository, changeset_revision, include_date=True, include_hash=True ): + """ + Return a string consisting of the human read-able changeset rev and the changeset revision string + which includes the revision date if the receive include_date is True. + """ + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + return get_revision_label_from_ctx( ctx, include_date=include_date, include_hash=include_hash ) + else: + if include_hash: + return "-1:%s" % changeset_revision + else: + return "-1" + +def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None, + include_date=True, include_hash=True ): + if repository is None: + repository = repository_metadata.repository + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + if include_date: + changeset_revision_date = get_readable_ctx_date( ctx ) + if include_hash: + label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date ) + else: + label = "%s (%s)" % ( str( ctx.rev() ), changeset_revision_date ) + else: + if include_hash: + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + label = "%s" % str( ctx.rev() ) + else: + rev = '-1' + if include_hash: + label = "-1:%s" % changeset_revision + else: + label = "-1" + return rev, label, changeset_revision + +def get_revision_label_from_ctx( ctx, include_date=True, include_hash=True ): + if include_date: + if include_hash: + return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) ) + else: + return '%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), str( get_readable_ctx_date( ctx ) ) ) + else: + if include_hash: + return '%s:%s' % ( str( ctx.rev() ), str( ctx ) ) + else: + return '%s' % str( ctx.rev() ) + +def get_rev_label_from_changeset_revision( repo, changeset_revision, include_date=True, include_hash=True ): + """ + Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash + which includes the revision date if the receive include_date is True. + """ + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = get_revision_label_from_ctx( ctx, include_date=include_date ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + return rev, label diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -8,6 +8,7 @@ from galaxy.datatypes import checkers from tool_shed.util import commit_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc @@ -212,7 +213,7 @@ archive_file_path = os.path.join( file_path, archive_file_name ) archive = tarfile.open( archive_file_path, 'r:*' ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 ok, error_message = commit_util.check_archive( repository, archive ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -15,6 +15,7 @@ from tool_shed.util import common_util from tool_shed.util import common_install_util from tool_shed.util import container_util +from tool_shed.util import hg_util from tool_shed.util import readme_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util @@ -347,7 +348,7 @@ # changeset revision in the received repository's changelog (up to the received changeset revision) to see if it is contained in the # skip_tool_test table. If it is, but is not associated with a repository_metadata record, reset that skip_tool_test record to the # newly created repository_metadata record. - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) skip_tool_test = suc.get_skip_tool_test_by_changeset_revision( trans, changeset_hash ) @@ -1048,7 +1049,7 @@ def get_latest_repository_metadata( trans, decoded_repository_id, downloadable=False ): """Get last metadata defined for a specified repository from the database.""" repository = trans.sa_session.query( trans.model.Repository ).get( decoded_repository_id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) if downloadable: changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) else: @@ -1121,21 +1122,6 @@ repository_metadata_revisions.append( metadata_revision ) return repository_metadata_revisions -def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ): - if repository is None: - repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - changeset_revision = repository_metadata.changeset_revision - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - changeset_revision_date = suc.get_readable_ctx_date( ctx ) - rev = '%04d' % ctx.rev() - label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - return rev, label, changeset_revision - def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: @@ -1294,7 +1280,7 @@ log.debug( error_message ) is_valid = False return repository_dependency_tup, is_valid, error_message - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( app ) ) # The received changeset_revision may be None since defining it in the dependency definition is optional. # If this is the case, the default will be to set it's value to the repository dependency tip revision. # This probably occurs only when handling circular dependency definitions. @@ -1360,7 +1346,7 @@ """ if repository.deleted: return ( None, False ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) # Get the latest installable changeset revision since that is all that is currently configured for testing. latest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) if latest_installable_changeset_revision not in [ None, suc.INITIAL_CHANGELOG_HASH ]: @@ -1797,7 +1783,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. @@ -1978,7 +1964,7 @@ encoded_id = trans.security.encode_id( repository.id ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, changeset_revision=repository.tip( trans.app ), diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -9,6 +9,7 @@ from galaxy.util import unicodify import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util +from tool_shed.util import hg_util eggs.require( 'mercurial' ) @@ -25,7 +26,7 @@ if trans.webapp.name == 'galaxy': can_use_disk_files = True else: - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision readme_files_dict = {} @@ -74,7 +75,7 @@ readme_files_dict[ readme_file_name ] = text_of_reasonable_length else: # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest. - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) if ctx: fctx = suc.get_file_context_from_ctx( ctx, readme_file_name ) if fctx and fctx not in [ 'DELETED' ]: diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -9,6 +9,7 @@ from tool_shed.util import common_install_util from tool_shed.util import container_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import tool_util @@ -532,7 +533,7 @@ else: # The repository changeset_revision is no longer installable, so see if there's been an update. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision ) repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, trans.security.encode_id( repository.id ), diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -3,6 +3,7 @@ import os import re import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import import_util from galaxy import util from galaxy.web.form_builder import build_select_field @@ -47,7 +48,7 @@ # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. The hg # purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll remove unknown files # and empty directories. This is not currently used because it is not supported in the mercurial API. - repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), path=repository.repo_path( trans.app ) ) fp = repo.opener( 'hgrc', 'wb' ) fp.write( '[paths]\n' ) fp.write( 'default = .\n' ) @@ -83,7 +84,7 @@ if not os.path.exists( repository_path ): os.makedirs( repository_path ) # Create the local repository. - repo = hg.repository( suc.get_configured_ui(), repository_path, create=True ) + repo = hg.repository( hg_util.get_configured_ui(), repository_path, create=True ) # Add an entry in the hgweb.config file for the local repository. lhs = "repos/%s/%s" % ( repository.user.username, repository.name ) trans.app.hgweb_config_manager.add_entry( lhs, repository_path ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/review_util.py --- a/lib/tool_shed/util/review_util.py +++ b/lib/tool_shed/util/review_util.py @@ -3,6 +3,7 @@ from galaxy import eggs from galaxy.model.orm import and_ from galaxy.util.odict import odict +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc eggs.require( 'mercurial' ) @@ -58,13 +59,13 @@ def get_previous_repository_reviews( trans, repository, changeset_revision ): """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] previous_reviews_dict = odict() for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) if previous_changeset_revision in reviewed_revision_hashes: - previous_rev, previous_changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) + previous_rev, previous_changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, trans.security.encode_id( repository.id ), previous_changeset_revision ) @@ -93,7 +94,7 @@ def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -4,9 +4,6 @@ import shutil import string import tempfile -from datetime import datetime -from time import gmtime -from time import strftime from galaxy import util from galaxy.util import asbool from galaxy.util import json @@ -19,6 +16,7 @@ import sqlalchemy.orm.exc from tool_shed.util import common_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import xml_util import tool_shed.repository_types.util as rt_util from xml.etree import ElementTree as XmlET @@ -143,7 +141,7 @@ def changeset_is_valid( app, repository, changeset_revision ): """Make sure a changeset hash is valid for a specified repository.""" - repo = hg.repository( get_configured_ui(), repository.repo_path( app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( app ) ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) if changeset_revision == changeset_hash: @@ -167,7 +165,7 @@ def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" try: - commands.clone( get_configured_ui(), + commands.clone( hg_util.get_configured_ui(), str( repository_clone_url ), dest=str( repository_file_dir ), pull=True, @@ -469,14 +467,6 @@ except sqlalchemy.orm.exc.NoResultFound: return None -def get_changectx_for_changeset( repo, changeset_revision, **kwd ): - """Retrieve a specified changectx from a repository.""" - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == changeset_revision: - return ctx - return None - def get_config( config_file, repo, ctx, dir ): """Return the latest version of config_filename from the repository manifest.""" config_file = strip_path( config_file ) @@ -496,16 +486,6 @@ return os.path.abspath( os.path.join( root, name ) ) return None -def get_configured_ui(): - """Configure any desired ui settings.""" - _ui = ui.ui() - # The following will suppress all messages. This is - # the same as adding the following setting to the repo - # hgrc file' [ui] section: - # quiet = True - _ui.setconfig( 'ui', 'quiet', True ) - return _ui - def get_ctx_rev( app, tool_shed_url, name, owner, changeset_revision ): """ Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the @@ -539,7 +519,7 @@ if repository_metadata: return repository_metadata # The installable changeset_revision may have been changed because it was "moved ahead" in the repository changelog. - repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) updated_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision=changeset_revision ) if updated_changeset_revision: repository_metadata = get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, updated_changeset_revision ) @@ -590,7 +570,7 @@ # record, so updates must be necessary. defined_repository = get_repository_by_name_and_owner( trans.app, name, owner ) defined_repo_dir = defined_repository.repo_path( trans.app ) - defined_repo = hg.repository( get_configured_ui(), defined_repo_dir ) + defined_repo = hg.repository( hg_util.get_configured_ui(), defined_repo_dir ) updated_changeset_revision = \ get_next_downloadable_changeset_revision( defined_repository, defined_repo, @@ -799,7 +779,7 @@ changeset_tups = [] for repository_metadata in metadata_revisions: changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() else: @@ -913,13 +893,6 @@ return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) -def get_readable_ctx_date( ctx ): - """Convert the date of the changeset (the received ctx) to a human-readable date.""" - t, tz = ctx.date() - date = datetime( *gmtime( float( t ) - tz )[ :6 ] ) - ctx_date = date.strftime( "%Y-%m-%d" ) - return ctx_date - def get_repo_info_tuple_contents( repo_info_tuple ): """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: @@ -1211,38 +1184,6 @@ reversed_changelog.insert( 0, changeset ) return reversed_changelog -def get_revision_label( trans, repository, changeset_revision, include_date=True ): - """ - Return a string consisting of the human read-able changeset rev and the changeset revision string - which includes the revision date if the receive include_date is True. - """ - repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - return get_revision_label_from_ctx( ctx, include_date=include_date ) - else: - return "-1:%s" % changeset_revision - -def get_revision_label_from_ctx( ctx, include_date=True ): - if include_date: - return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ - ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) ) - return '%s:%s' % ( str( ctx.rev() ), str( ctx ) ) - -def get_rev_label_from_changeset_revision( repo, changeset_revision, include_date=True ): - """ - Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash - which includes the revision date if the receive include_date is True. - """ - ctx = get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - rev = '%04d' % ctx.rev() - label = get_revision_label_from_ctx( ctx, include_date=include_date ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - return rev, label - def get_shed_tool_conf_dict( app, shed_tool_conf ): """Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict associated with the file.""" for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ): @@ -1434,7 +1375,7 @@ """ repository = get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the upper bound changeset revision. upper_bound_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) # Build the list of changeset revision hashes defining each available update up to, but excluding, upper_bound_changeset_revision. @@ -1487,7 +1428,7 @@ that was included in the change set. """ repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) sharable_link = generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None ) smtp_server = trans.app.config.smtp_server if smtp_server and ( new_repo_alert or repository.email_alerts ): @@ -1510,7 +1451,7 @@ template = new_repo_email_alert_template else: template = email_alert_template - display_date = get_readable_ctx_date( ctx ) + display_date = hg_util.get_readable_ctx_date( ctx ) admin_body = string.Template( template ).safe_substitute( host=trans.request.host, sharable_link=sharable_link, repository_name=repository.name, @@ -1859,7 +1800,7 @@ # I = ignored # It would be nice if we could use mercurial's purge extension to remove untracked files. The problem is that # purging is not supported by the mercurial API. - commands.update( get_configured_ui(), repo, rev=ctx_rev ) + commands.update( hg_util.get_configured_ui(), repo, rev=ctx_rev ) def update_tool_shed_repository_status( app, tool_shed_repository, status, error_message=None ): """Update the status of a tool shed repository in the process of being installed into Galaxy.""" diff -r 6e2eaa8626b218edb9e738a3b489fede6c627b85 -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -15,6 +15,7 @@ from galaxy.web.form_builder import SelectField from galaxy.tools.actions.upload import UploadToolAction from tool_shed.util import common_util +from tool_shed.util import hg_util from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc from xml.etree import ElementTree as XmlET @@ -538,7 +539,7 @@ """ repository = suc.get_repository_by_id( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Initialize the tool lineage version_lineage = [ guid ] # Get all ancestor guids of the received guid. @@ -637,7 +638,7 @@ def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, repository_id, changeset_revision, tool_config_filename, work_dir ): tool = None message = '' - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) # We're not currently doing anything with the returned list of deleted_sample_files here. It is intended to help handle sample files that are in # the manifest, but have been deleted from disk. sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) @@ -866,7 +867,7 @@ original_tool_data_path = trans.app.config.tool_data_path repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) message = '' tool = None can_use_disk_file = False This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dcfd828a229e/ Changeset: dcfd828a229e Branch: next-stable User: Jeremy Goecks Date: 2014-04-10 23:21:00 Summary: Updates to Sweepster to get it working again. Affected #: 9 files diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -979,7 +979,7 @@ if option[2]: # Found selected option. value = option[1] - d[ 'value' ] = options + d[ 'value' ] = value return d diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -42,7 +42,7 @@ num_samples: 5 }, - initialize: function() { + initialize: function(options) { this.attributes.html = unescape(this.attributes.html); }, @@ -124,6 +124,8 @@ outputs: [] }, + urlRoot: galaxy_config.root + 'api/tools', + initialize: function(options) { // Set parameters. @@ -133,7 +135,16 @@ }))); }, - urlRoot: galaxy_config.root + 'api/tools', + /** + * + */ + toJSON: function() { + var rval = Backbone.Model.prototype.toJSON.call(this); + + // Convert inputs to JSON manually. + rval.inputs = this.get('inputs').map(function(i) { return i.toJSON(); }); + return rval; + }, /** * Removes inputs of a particular type; this is useful because not all inputs can be handled by diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},urlRoot:galaxy_config.root+"api/tools",remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){this.$el.append(Handlebars.templates.tool_link(this.model.toJSON()));return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){this.$el.append(Handlebars.templates.tool_link(this.model.toJSON()));return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("value")===undefined){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("value")===undefined){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSetting:d,ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/packed/viz/sweepster.js --- a/static/scripts/packed/viz/sweepster.js +++ b/static/scripts/packed/viz/sweepster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(m,q,f,o,h,g,d){var n=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.Model.extend({defaults:{tool:null,tree_data:null},initialize:function(s){var r=this;this.get("tool").get("inputs").each(function(t){t.on("change:min change:max change:num_samples",function(u){if(u.get("in_ptree")){r.set_tree_data()}},r);t.on("change:in_ptree",function(u){if(u.get("in_ptree")){r.add_param(u)}else{r.remove_param(u)}r.set_tree_data()},r)});if(s.config){m.each(s.config,function(u){var t=r.get("tool").get("inputs").find(function(v){return v.get("name")===u.name});r.add_param(t);t.set(u)})}},add_param:function(r){if(r.get("ptree_index")){return}r.set("in_ptree",true);r.set("ptree_index",this.get_tree_params().length)},remove_param:function(r){r.set("in_ptree",false);r.set("ptree_index",null);m(this.get_tree_params()).each(function(s,t){s.set("ptree_index",t+1)})},set_tree_data:function(){var s=m.map(this.get_tree_params(),function(u){return{param:u,samples:u.get_samples()}});var r=0,t=function(x,u){var z=x[u],y=z.param,w=y.get("label"),v=z.samples;if(x.length-1===u){return m.map(v,function(A){return{id:r++,name:A,param:y,value:A}})}return m.map(v,function(A){return{id:r++,name:A,param:y,value:A,children:t(x,u+1)}})};this.set("tree_data",{name:"Root",id:r++,children:(s.length!==0?t(s,0):null)})},get_tree_params:function(){return m(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(r){return r.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(r,s){return r*s.get_samples().length},1)},get_node_settings:function(v){var t=this.get("tool").get_inputs_dict();var w=v.parent;if(w){while(w.depth!==0){t[w.param.get("name")]=w.value;w=w.parent}}var r=this,s=function(y,x){if(y.param){x[y.param.get("name")]=y.value}if(!y.children){return new n({inputs:r.get("tool").get("inputs"),values:x})}else{return m.flatten(m.map(y.children,function(z){return s(z,m.clone(x))}))}},u=s(v,t);if(!m.isArray(u)){u=[u]}return u},get_connected_nodes:function(t){var u=function(v){if(!v.children){return v}else{return m.flatten([v,m.map(v.children,function(w){return u(w)})])}};var s=[],r=t.parent;while(r){s.push(r);r=r.parent}return m.flatten([s,u(t)])},get_leaf:function(s){var t=this.get("tree_data"),r=function(u){return m.find(u,function(v){return s[v.param.get("name")]===v.value})};while(t.children){t=r(t.children)}return t},toJSON:function(){return this.get_tree_params().map(function(r){return{name:r.get("name"),min:r.get("min"),max:r.get("max"),num_samples:r.get("num_samples")}})}});var c=Backbone.Model.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},initialize:function(r){this.set("regions",new o.GenomeRegionCollection(r.regions));if(r.track){var s=m.extend({data_url:galaxy_config.root+"dummy1",converted_datasets_state_url:galaxy_config.root+"dummy2"},r.track);this.set("track",h.object_from_template(s,{},null))}},same_settings:function(r){var s=this.get("settings"),t=r.get("settings");for(var u in s){if(!t[u]||s[u]!==t[u]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=o.Visualization.extend({defaults:m.extend({},o.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),initialize:function(r){this.set("dataset",new d.Dataset(r.dataset));this.set("tool",new g.Tool(r.tool));this.set("regions",new o.GenomeRegionCollection(r.regions));this.set("tracks",new SweepsterTrackCollection(r.tracks));var s=this.get("tool");this.set("tool_with_samplable_inputs",s);s.remove_inputs(["data","hidden_data","conditional"]);this.set("parameter_tree",new p({tool:s,config:r.tree_config}))},add_track:function(r){this.get("tracks").add(r)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(r){this.canvas_manager=r.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var w=this.model.get("settings"),s=w.get("values"),u=$("<td/>").addClass("settings").appendTo(this.$el),t=$("<div/>").addClass("track-info").hide().appendTo(u);t.append($("<div/>").css("font-weight","bold").text("Track Settings"));w.get("inputs").each(function(y){t.append(y.get("label")+": "+s[y.get("name")]+"<br/>")});var r=this,x=$("<button/>").appendTo(t).text("Run on complete dataset").click(function(){t.toggle();r.trigger("run_on_dataset",w)});var v=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){t.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){r.$el.remove();$(".tooltip").remove()}}]);u.prepend(v.$el);this.model.get("regions").each(function(){r.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_config.root+"images/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var s=this,r=this.model.get("track"),u=this.model.get("regions"),t=this.$el.find("td.tile");if(!r){return}$.when(r.data_manager.data_is_ready()).then(function(v){u.each(function(y,x){var w=y.length()/s.TILE_LEN,A=1/w,z=s.model.get("mode");$.when(r.data_manager.get_data(y,z,w,{})).then(function(C){var B=s.canvas_manager.new_canvas();B.width=s.TILE_LEN;B.height=r.get_canvas_height(C,z,A,B.width);r.draw_tile(C,B.getContext("2d"),z,w,y,A);$(t[x]).empty().append(B)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(r){this.$el=r.tool_row;this.render()},render:function(){var s=this.model,w=s.get("type"),y=this.$el.find(".form-row-input"),u=null;y.find(":input").change(function(){s.set("value",$(this).val())});if(s instanceof g.IntegerToolParameter){u=$(m.template(this.number_input_template,this.model.toJSON()))}else{if(s instanceof g.SelectToolParameter){var t=m.map(this.$el.find("select option"),function(z){return $(z).val()}),v=t.join(", ");u=$(m.template(this.select_input_template,{options:v}))}}u.insertAfter(y);var r=this,x=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){s.set("in_ptree",true);y.hide();u.show();$(this).hide();r.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){s.set("in_ptree",false);u.hide();y.show();$(this).hide();r.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(x.$el);if(s.get("in_ptree")){y.hide();r.$el.find(".icon-button.plus-button").hide()}else{r.$el.find(".icon-button.toggle").hide();u.hide()}m.each(["min","max","num_samples"],function(z){u.find("."+z).change(function(){s.set(z,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(r){this.render()},render:function(){var t=new g.ToolFormView({model:this.model.get("tool")});t.render();this.$el.append(t.$el);var s=this,r=s.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(u){var v=new b({model:r.at(u),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(r){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var z=this.model.get_tree_params();if(!z.length){return}this.width=100*(2+z.length);this.height=15*this.model.get_num_leaves();var y=this;var x=q.layout.cluster().size([this.height,this.width-160]);var t=q.svg.diagonal().projection(function(A){return[A.y,A.x]});var r=x.nodes(this.model.get("tree_data"));var u=m.uniq(m.pluck(r,"y"));m.each(z,function(C,B){var A=u[B+1],D=$("#center").position().left;y.$el.append($("<div>").addClass("label").text(C.get("label")).css("left",A+D))});var s=q.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var w=s.selectAll("path.link").data(x.links(r)).enter().append("path").attr("class","link").attr("d",t);var v=s.selectAll("g.node").data(r).enter().append("g").attr("class","node").attr("transform",function(A){return"translate("+A.y+","+A.x+")"}).on("mouseover",function(B){var A=m.pluck(y.model.get_connected_nodes(B),"id");v.filter(function(C){return m.find(A,function(D){return D===C.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){v.style("fill","#000")});v.append("circle").attr("r",9);v.append("text").attr("dx",function(A){return A.children?-12:12}).attr("dy",3).attr("text-anchor",function(A){return A.children?"end":"start"}).text(function(A){return A.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(s){this.canvas_manager=new o.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var r=this;this.model.get("tracks").each(function(t){t.get("track").view=r});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var x=new k({model:this.model.get("parameter_tree")});$("#left").append(x.$el);var A=this,u=A.model.get("regions"),y=$("<tr/>").appendTo(this.track_collection_container);u.each(function(B){y.append($("<th>").text(B.toString()))});y.children().first().attr("colspan",2);var v=$("<div>").addClass("tiles");$("#right").append(v.append(this.track_collection_container));A.model.get("tracks").each(function(B){A.add_track(B)});var z=$(this.helpText).addClass("help"),w=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tooltip").remove();z.remove()}}]);z.prepend(w.$el.css("float","right"));$("#center").append(z);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var t=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var s=["Squish","Pack"],r={};m.each(s,function(B){r[B]=function(){A.model.set("default_mode",B);A.model.get("tracks").each(function(C){C.set("mode",B)})}});make_popupmenu(t.$el.find(".chevron-expand"),r);t.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(t.$el)},run_tool_on_dataset:function(s){var r=this.model.get("tool"),u=r.get("name"),t=this.model.get("dataset");r.set_input_values(s.get("values"));$.when(r.rerun(t)).then(function(v){});show_modal("Running "+u+" on complete dataset",u+" is running on dataset '"+t.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(u){var s=this,t=this.model.get("parameter_tree");s.model.add_track(u);var r=new l({model:u,canvas_manager:s.canvas_manager});r.on("run_on_dataset",s.run_tool_on_dataset,s);s.track_collection_container.append(r.$el);r.$el.hover(function(){var w=t.get_leaf(u.get("settings").get("values"));var v=m.pluck(t.get_connected_nodes(w),"id");q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(x){return m.find(v,function(y){return y===x.id})!==undefined}).style("fill","#f00")},function(){q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return u},handle_node_clicks:function(){var r=this,s=this.model.get("parameter_tree"),u=this.model.get("regions"),t=q.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");t.on("click",function(A,x){var w=r.model.get("tool"),z=r.model.get("dataset"),y=s.get_node_settings(A),v=$.Deferred();if(y.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+r.model.get("tool").get("name")+" with "+y.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();v.resolve(false)}})}else{v.resolve(true)}$.when(v).then(function(B){if(!B){return}var C=m.map(y,function(D){var E=new c({settings:D,regions:u,mode:r.model.get("default_mode")});r.add_track(E);return E});m.each(C,function(E,D){setTimeout(function(){w.set_input_values(E.get("settings").get("values"));$.when(w.rerun(z,u)).then(function(G){var H=G.first(),I=H.get("track_config");I.dataset=H;I.tool=null;var F=h.object_from_template(I,r,null);F.init_for_tool_data();F.prefs.block_color=r.block_color;F.prefs.reverse_strand_color=r.reverse_strand_color;E.set("track",F)})},D*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data","utils/config"],function(q,p,e,j,m,n,r,o){var k=Backbone.Model.extend({defaults:{inputs:null,values:null}});var a=Backbone.Model.extend({defaults:{tool:null,tree_data:null},initialize:function(t){var s=this;this.get("tool").get("inputs").each(function(u){u.on("change:min change:max change:num_samples",function(v){if(v.get("in_ptree")){s.set_tree_data()}},s);u.on("change:in_ptree",function(v){if(v.get("in_ptree")){s.add_param(v)}else{s.remove_param(v)}s.set_tree_data()},s)});if(t.config){q.each(t.config,function(v){var u=s.get("tool").get("inputs").find(function(w){return w.get("name")===v.name});s.add_param(u);u.set(v)})}},add_param:function(s){if(s.get("ptree_index")){return}s.set("in_ptree",true);s.set("ptree_index",this.get_tree_params().length)},remove_param:function(s){s.set("in_ptree",false);s.set("ptree_index",null);q(this.get_tree_params()).each(function(t,u){t.set("ptree_index",u+1)})},set_tree_data:function(){var t=q.map(this.get_tree_params(),function(v){return{param:v,samples:v.get_samples()}});var s=0,u=function(y,v){var A=y[v],z=A.param,x=z.get("label"),w=A.samples;if(y.length-1===v){return q.map(w,function(B){return{id:s++,name:B,param:z,value:B}})}return q.map(w,function(B){return{id:s++,name:B,param:z,value:B,children:u(y,v+1)}})};this.set("tree_data",{name:"Root",id:s++,children:(t.length!==0?u(t,0):null)})},get_tree_params:function(){return q(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(s){return s.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(s,t){return s*t.get_samples().length},1)},get_node_settings:function(w){var u=this.get("tool").get_inputs_dict();var x=w.parent;if(x){while(x.depth!==0){u[x.param.get("name")]=x.value;x=x.parent}}var s=this,t=function(z,y){if(z.param){y[z.param.get("name")]=z.value}if(!z.children){return new k({inputs:s.get("tool").get("inputs"),values:y})}else{return q.flatten(q.map(z.children,function(A){return t(A,q.clone(y))}))}},v=t(w,u);if(!q.isArray(v)){v=[v]}return v},get_connected_nodes:function(u){var v=function(w){if(!w.children){return w}else{return q.flatten([w,q.map(w.children,function(x){return v(x)})])}};var t=[],s=u.parent;while(s){t.push(s);s=s.parent}return q.flatten([t,v(u)])},get_leaf:function(t){var u=this.get("tree_data"),s=function(v){return q.find(v,function(w){return t[w.param.get("name")]===w.value})};while(u.children){u=s(u.children)}return u},toJSON:function(){return this.get_tree_params().map(function(s){return{name:s.get("name"),min:s.get("min"),max:s.get("max"),num_samples:s.get("num_samples")}})}});var d=Backbone.Model.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},initialize:function(s){this.set("regions",s.regions);if(s.track){var t=q.extend({data_url:galaxy_config.root+"dummy1",converted_datasets_state_url:galaxy_config.root+"dummy2"},s.track);this.set("track",m.object_from_template(t,{},null))}},same_settings:function(s){var t=this.get("settings"),u=s.get("settings");for(var v in t){if(!u[v]||t[v]!==u[v]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var l=Backbone.Collection.extend({model:d});var c=j.Visualization.extend({defaults:q.extend({},j.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),initialize:function(s){this.set("dataset",new r.Dataset(s.dataset));this.set("tool",new n.Tool(s.tool));this.set("regions",new j.GenomeRegionCollection(s.regions));this.set("tracks",new l(s.tracks));var t=this.get("tool");this.set("tool_with_samplable_inputs",t);t.remove_inputs(["data","hidden_data","conditional","text"]);this.set("parameter_tree",new a({tool:t,config:s.tree_config}))},add_track:function(s){this.get("tracks").add(s)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var h=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(s){this.canvas_manager=s.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var x=this.model.get("settings"),t=x.get("values"),v=$("<td/>").addClass("settings").appendTo(this.$el),u=$("<div/>").addClass("track-info").hide().appendTo(v);u.append($("<div/>").css("font-weight","bold").text("Track Settings"));x.get("inputs").each(function(z){u.append(z.get("label")+": "+t[z.get("name")]+"<br/>")});var s=this,y=$("<button/>").appendTo(u).text("Run on complete dataset").click(function(){u.toggle();s.trigger("run_on_dataset",x)});var w=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){u.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){s.$el.remove();$(".tooltip").remove()}}]);v.prepend(w.$el);this.model.get("regions").each(function(){s.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_config.root+"images/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var t=this,s=this.model.get("track"),v=this.model.get("regions"),u=this.$el.find("td.tile");if(!s){return}$.when(s.data_manager.data_is_ready()).then(function(w){v.each(function(z,y){var x=z.length()/t.TILE_LEN,B=1/x,A=t.model.get("mode");$.when(s.data_manager.get_data(z,A,x,{})).then(function(D){var C=t.canvas_manager.new_canvas();C.width=t.TILE_LEN;C.height=s.get_canvas_height(D,A,B,C.width);s.draw_tile(D,C.getContext("2d"),A,z,B);$(u[y]).empty().append(C)})})})}});var g=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(s){this.$el=s.tool_row;this.render()},render:function(){var t=this.model,x=t.get("type"),z=this.$el.find(".form-row-input"),v=null;z.find(":input").change(function(){t.set("value",$(this).val())});if(t instanceof n.IntegerToolParameter){v=$(q.template(this.number_input_template,this.model.toJSON()))}else{if(t instanceof n.SelectToolParameter){var u=q.map(this.$el.find("select option"),function(A){return $(A).val()}),w=u.join(", ");v=$(q.template(this.select_input_template,{options:w}))}}v.insertAfter(z);var s=this,y=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){t.set("in_ptree",true);z.hide();v.show();$(this).hide();s.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){t.set("in_ptree",false);v.hide();z.show();$(this).hide();s.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(y.$el);if(t.get("in_ptree")){z.hide();s.$el.find(".icon-button.plus-button").hide()}else{s.$el.find(".icon-button.toggle").hide();v.hide()}q.each(["min","max","num_samples"],function(A){v.find("."+A).change(function(){t.set(A,parseFloat($(this).val()))})})}});var i=Backbone.View.extend({className:"tree-design",initialize:function(s){this.render()},render:function(){var u=new n.ToolFormView({model:this.model.get("tool")});u.render();this.$el.append(u.$el);var t=this,s=t.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(v){var w=new g({model:s.at(v),tool_row:$(this)})})}});var b=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(s){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var A=this.model.get_tree_params();if(!A.length){return}this.width=100*(2+A.length);this.height=15*this.model.get_num_leaves();var z=this;var y=p.layout.cluster().size([this.height,this.width-160]);var u=p.svg.diagonal().projection(function(B){return[B.y,B.x]});var s=y.nodes(this.model.get("tree_data"));var v=q.uniq(q.pluck(s,"y"));q.each(A,function(D,C){var B=v[C+1],E=$("#center").position().left;z.$el.append($("<div>").addClass("label").text(D.get("label")).css("left",B+E))});var t=p.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var x=t.selectAll("path.link").data(y.links(s)).enter().append("path").attr("class","link").attr("d",u);var w=t.selectAll("g.node").data(s).enter().append("g").attr("class","node").attr("transform",function(B){return"translate("+B.y+","+B.x+")"}).on("mouseover",function(C){var B=q.pluck(z.model.get_connected_nodes(C),"id");w.filter(function(D){return q.find(B,function(E){return E===D.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){w.style("fill","#000")});w.append("circle").attr("r",9);w.append("text").attr("dx",function(B){return B.children?-12:12}).attr("dy",3).attr("text-anchor",function(B){return B.children?"end":"start"}).text(function(B){return B.name})}});var f=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(t){this.canvas_manager=new j.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new b({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var s=this;this.model.get("tracks").each(function(u){u.get("track").view=s});this.config=o.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},],{})},render:function(){var y=new i({model:this.model.get("parameter_tree")});$("#left").append(y.$el);var B=this,v=B.model.get("regions"),z=$("<tr/>").appendTo(this.track_collection_container);v.each(function(C){z.append($("<th>").text(C.toString()))});z.children().first().attr("colspan",2);var w=$("<div>").addClass("tiles");$("#right").append(w.append(this.track_collection_container));B.model.get("tracks").each(function(C){B.add_track(C)});var A=$(this.helpText).addClass("help"),x=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tooltip").remove();A.remove()}}]);A.prepend(x.$el.css("float","right"));$("#center").append(A);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var u=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var t=["Squish","Pack"],s={};q.each(t,function(C){s[C]=function(){B.model.set("default_mode",C);B.model.get("tracks").each(function(D){D.set("mode",C)})}});make_popupmenu(u.$el.find(".chevron-expand"),s);u.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(u.$el)},get_base_color:function(s){return this.config.get_value(s.toLowerCase()+"_color")||this.config.get_value("n_color")},run_tool_on_dataset:function(t){var s=this.model.get("tool"),v=s.get("name"),u=this.model.get("dataset");s.set_input_values(t.get("values"));$.when(s.rerun(u)).then(function(w){});show_modal("Running "+v+" on complete dataset",v+" is running on dataset '"+u.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(v){var t=this,u=this.model.get("parameter_tree");t.model.add_track(v);var s=new h({model:v,canvas_manager:t.canvas_manager});s.on("run_on_dataset",t.run_tool_on_dataset,t);t.track_collection_container.append(s.$el);s.$el.hover(function(){var x=u.get_leaf(v.get("settings").get("values"));var w=q.pluck(u.get_connected_nodes(x),"id");p.select(t.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(y){return q.find(w,function(z){return z===y.id})!==undefined}).style("fill","#f00")},function(){p.select(t.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return v},handle_node_clicks:function(){var s=this,t=this.model.get("parameter_tree"),v=this.model.get("regions"),u=p.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");u.on("click",function(B,y){var x=s.model.get("tool"),A=s.model.get("dataset"),z=t.get_node_settings(B),w=$.Deferred();if(z.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+s.model.get("tool").get("name")+" with "+z.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();w.resolve(false)}})}else{w.resolve(true)}$.when(w).then(function(C){if(!C){return}var D=q.map(z,function(E){var F=new d({settings:E,regions:v,mode:s.model.get("default_mode")});s.add_track(F);return F});q.each(D,function(F,E){setTimeout(function(){x.set_input_values(F.get("settings").get("values"));$.when(x.rerun(A,v)).then(function(H){var I=H.first(),J=I.get("track_config");J.dataset=I;J.tool=null;J.prefs=s.config.to_key_value_dict();var G=m.object_from_template(J,s,null);G.init_for_tool_data();F.set("track",G)})},E*10000)})})})}});return{SweepsterVisualization:c,SweepsterVisualizationView:f}}); \ No newline at end of file diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -304,6 +304,7 @@ }); return { + ConfigSetting: ConfigSetting, ConfigSettingCollection: ConfigSettingCollection, ConfigSettingCollectionView: ConfigSettingCollectionView }; diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -3,8 +3,8 @@ * genomic visualization. */ -define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], - function(_, d3, util, visualization, tracks, tools, data) { +define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data", "utils/config"], + function(_, d3, util, visualization, tracks, tools, data, config) { /** * A collection of tool input settings. Object is useful for keeping a list of settings @@ -257,7 +257,7 @@ }, initialize: function(options) { - this.set('regions', new visualization.GenomeRegionCollection(options.regions)); + this.set('regions', options.regions); if (options.track) { // FIXME: find a better way to deal with needed URLs: var track_config = _.extend({ @@ -310,12 +310,12 @@ this.set('dataset', new data.Dataset(options.dataset)); this.set('tool', new tools.Tool(options.tool)); this.set('regions', new visualization.GenomeRegionCollection(options.regions)); - this.set('tracks', new SweepsterTrackCollection(options.tracks)); + this.set('tracks', new TrackCollection(options.tracks)); var tool_with_samplable_inputs = this.get('tool'); this.set('tool_with_samplable_inputs', tool_with_samplable_inputs); // Remove complex parameters for now. - tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional' ] ); + tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional', 'text' ] ); this.set('parameter_tree', new ToolParameterTree({ tool: tool_with_samplable_inputs, @@ -430,7 +430,7 @@ var canvas = self.canvas_manager.new_canvas(); canvas.width = self.TILE_LEN; canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width); - track.draw_tile(tile_data, canvas.getContext('2d'), mode, resolution, region, w_scale); + track.draw_tile(tile_data, canvas.getContext('2d'), mode, region, w_scale); $(tile_containers[index]).empty().append(canvas); }); }); @@ -680,8 +680,18 @@ }); // Set block, reverse strand block colors; these colors will be used for all tracks. - this.block_color = util.get_random_color(); - this.reverse_strand_color = util.get_random_color( [ this.block_color, "#ffffff" ] ); + this.config = config.ConfigSettingCollection.from_models_and_saved_values( + [ + { key: 'name', label: 'Name', type: 'text', default_value: '' }, + { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, + { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" }, + { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" }, + { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" }, + { key: 'n_color', label: 'N Color', type: 'color', default_value: "#AAAAAA" }, + { key: 'block_color', label: 'Block color', type: 'color' }, + { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' }, + ], {} + ); }, render: function() { @@ -792,6 +802,11 @@ $("#right .unified-panel-header-inner").append(menu.$el); }, + get_base_color: function(base) { + return this.config.get_value(base.toLowerCase() + '_color') || + this.config.get_value('n_color'); + }, + run_tool_on_dataset: function(settings) { var tool = this.model.get('tool'), tool_name = tool.get('name'), @@ -904,14 +919,12 @@ // the tool parameters and parameter tree. track_config.tool = null; + track_config.prefs = self.config.to_key_value_dict(); + // Create and add track for output dataset. var track_obj = tracks.object_from_template(track_config, self, null); track_obj.init_for_tool_data(); - // Set track block colors. - track_obj.prefs.block_color = self.block_color; - track_obj.prefs.reverse_strand_color = self.reverse_strand_color; - pm_track.set('track', track_obj); }); }, index * 10000); diff -r 9854b48f89026970f99b004d465ffa63aad54aad -r dcfd828a229e5d43d1610cc510d71088620a1112 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2243,7 +2243,7 @@ on_click_fn: function(track) { var template = '<strong>Tool</strong>: <%= track.tool.get("name") %><br/>' + - '<strong>Dataset</strong>: <%= track.config.get("name") %><br/>' + + '<strong>Dataset</strong>: <%= track.config.get_value("name") %><br/>' + '<strong>Region(s)</strong>: <select name="regions">' + '<option value="cur">current viewing area</option>' + '<option value="bookmarks">bookmarks</option>' + https://bitbucket.org/galaxy/galaxy-central/commits/5d666f5fae29/ Changeset: 5d666f5fae29 User: Jeremy Goecks Date: 2014-04-10 23:21:38 Summary: Merge next-stable branch to default. Affected #: 9 files diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -979,7 +979,7 @@ if option[2]: # Found selected option. value = option[1] - d[ 'value' ] = options + d[ 'value' ] = value return d diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -42,7 +42,7 @@ num_samples: 5 }, - initialize: function() { + initialize: function(options) { this.attributes.html = unescape(this.attributes.html); }, @@ -124,6 +124,8 @@ outputs: [] }, + urlRoot: galaxy_config.root + 'api/tools', + initialize: function(options) { // Set parameters. @@ -133,7 +135,16 @@ }))); }, - urlRoot: galaxy_config.root + 'api/tools', + /** + * + */ + toJSON: function() { + var rval = Backbone.Model.prototype.toJSON.call(this); + + // Convert inputs to JSON manually. + rval.inputs = this.get('inputs').map(function(i) { return i.toJSON(); }); + return rval; + }, /** * Removes inputs of a particular type; this is useful because not all inputs can be handled by diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},urlRoot:galaxy_config.root+"api/tools",remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){this.$el.append(Handlebars.templates.tool_link(this.model.toJSON()));return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){this.$el.append(Handlebars.templates.tool_link(this.model.toJSON()));return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("value")===undefined){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("value")===undefined){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSetting:d,ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/packed/viz/sweepster.js --- a/static/scripts/packed/viz/sweepster.js +++ b/static/scripts/packed/viz/sweepster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(m,q,f,o,h,g,d){var n=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.Model.extend({defaults:{tool:null,tree_data:null},initialize:function(s){var r=this;this.get("tool").get("inputs").each(function(t){t.on("change:min change:max change:num_samples",function(u){if(u.get("in_ptree")){r.set_tree_data()}},r);t.on("change:in_ptree",function(u){if(u.get("in_ptree")){r.add_param(u)}else{r.remove_param(u)}r.set_tree_data()},r)});if(s.config){m.each(s.config,function(u){var t=r.get("tool").get("inputs").find(function(v){return v.get("name")===u.name});r.add_param(t);t.set(u)})}},add_param:function(r){if(r.get("ptree_index")){return}r.set("in_ptree",true);r.set("ptree_index",this.get_tree_params().length)},remove_param:function(r){r.set("in_ptree",false);r.set("ptree_index",null);m(this.get_tree_params()).each(function(s,t){s.set("ptree_index",t+1)})},set_tree_data:function(){var s=m.map(this.get_tree_params(),function(u){return{param:u,samples:u.get_samples()}});var r=0,t=function(x,u){var z=x[u],y=z.param,w=y.get("label"),v=z.samples;if(x.length-1===u){return m.map(v,function(A){return{id:r++,name:A,param:y,value:A}})}return m.map(v,function(A){return{id:r++,name:A,param:y,value:A,children:t(x,u+1)}})};this.set("tree_data",{name:"Root",id:r++,children:(s.length!==0?t(s,0):null)})},get_tree_params:function(){return m(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(r){return r.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(r,s){return r*s.get_samples().length},1)},get_node_settings:function(v){var t=this.get("tool").get_inputs_dict();var w=v.parent;if(w){while(w.depth!==0){t[w.param.get("name")]=w.value;w=w.parent}}var r=this,s=function(y,x){if(y.param){x[y.param.get("name")]=y.value}if(!y.children){return new n({inputs:r.get("tool").get("inputs"),values:x})}else{return m.flatten(m.map(y.children,function(z){return s(z,m.clone(x))}))}},u=s(v,t);if(!m.isArray(u)){u=[u]}return u},get_connected_nodes:function(t){var u=function(v){if(!v.children){return v}else{return m.flatten([v,m.map(v.children,function(w){return u(w)})])}};var s=[],r=t.parent;while(r){s.push(r);r=r.parent}return m.flatten([s,u(t)])},get_leaf:function(s){var t=this.get("tree_data"),r=function(u){return m.find(u,function(v){return s[v.param.get("name")]===v.value})};while(t.children){t=r(t.children)}return t},toJSON:function(){return this.get_tree_params().map(function(r){return{name:r.get("name"),min:r.get("min"),max:r.get("max"),num_samples:r.get("num_samples")}})}});var c=Backbone.Model.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},initialize:function(r){this.set("regions",new o.GenomeRegionCollection(r.regions));if(r.track){var s=m.extend({data_url:galaxy_config.root+"dummy1",converted_datasets_state_url:galaxy_config.root+"dummy2"},r.track);this.set("track",h.object_from_template(s,{},null))}},same_settings:function(r){var s=this.get("settings"),t=r.get("settings");for(var u in s){if(!t[u]||s[u]!==t[u]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=o.Visualization.extend({defaults:m.extend({},o.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),initialize:function(r){this.set("dataset",new d.Dataset(r.dataset));this.set("tool",new g.Tool(r.tool));this.set("regions",new o.GenomeRegionCollection(r.regions));this.set("tracks",new SweepsterTrackCollection(r.tracks));var s=this.get("tool");this.set("tool_with_samplable_inputs",s);s.remove_inputs(["data","hidden_data","conditional"]);this.set("parameter_tree",new p({tool:s,config:r.tree_config}))},add_track:function(r){this.get("tracks").add(r)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(r){this.canvas_manager=r.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var w=this.model.get("settings"),s=w.get("values"),u=$("<td/>").addClass("settings").appendTo(this.$el),t=$("<div/>").addClass("track-info").hide().appendTo(u);t.append($("<div/>").css("font-weight","bold").text("Track Settings"));w.get("inputs").each(function(y){t.append(y.get("label")+": "+s[y.get("name")]+"<br/>")});var r=this,x=$("<button/>").appendTo(t).text("Run on complete dataset").click(function(){t.toggle();r.trigger("run_on_dataset",w)});var v=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){t.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){r.$el.remove();$(".tooltip").remove()}}]);u.prepend(v.$el);this.model.get("regions").each(function(){r.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_config.root+"images/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var s=this,r=this.model.get("track"),u=this.model.get("regions"),t=this.$el.find("td.tile");if(!r){return}$.when(r.data_manager.data_is_ready()).then(function(v){u.each(function(y,x){var w=y.length()/s.TILE_LEN,A=1/w,z=s.model.get("mode");$.when(r.data_manager.get_data(y,z,w,{})).then(function(C){var B=s.canvas_manager.new_canvas();B.width=s.TILE_LEN;B.height=r.get_canvas_height(C,z,A,B.width);r.draw_tile(C,B.getContext("2d"),z,w,y,A);$(t[x]).empty().append(B)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(r){this.$el=r.tool_row;this.render()},render:function(){var s=this.model,w=s.get("type"),y=this.$el.find(".form-row-input"),u=null;y.find(":input").change(function(){s.set("value",$(this).val())});if(s instanceof g.IntegerToolParameter){u=$(m.template(this.number_input_template,this.model.toJSON()))}else{if(s instanceof g.SelectToolParameter){var t=m.map(this.$el.find("select option"),function(z){return $(z).val()}),v=t.join(", ");u=$(m.template(this.select_input_template,{options:v}))}}u.insertAfter(y);var r=this,x=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){s.set("in_ptree",true);y.hide();u.show();$(this).hide();r.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){s.set("in_ptree",false);u.hide();y.show();$(this).hide();r.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(x.$el);if(s.get("in_ptree")){y.hide();r.$el.find(".icon-button.plus-button").hide()}else{r.$el.find(".icon-button.toggle").hide();u.hide()}m.each(["min","max","num_samples"],function(z){u.find("."+z).change(function(){s.set(z,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(r){this.render()},render:function(){var t=new g.ToolFormView({model:this.model.get("tool")});t.render();this.$el.append(t.$el);var s=this,r=s.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(u){var v=new b({model:r.at(u),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(r){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var z=this.model.get_tree_params();if(!z.length){return}this.width=100*(2+z.length);this.height=15*this.model.get_num_leaves();var y=this;var x=q.layout.cluster().size([this.height,this.width-160]);var t=q.svg.diagonal().projection(function(A){return[A.y,A.x]});var r=x.nodes(this.model.get("tree_data"));var u=m.uniq(m.pluck(r,"y"));m.each(z,function(C,B){var A=u[B+1],D=$("#center").position().left;y.$el.append($("<div>").addClass("label").text(C.get("label")).css("left",A+D))});var s=q.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var w=s.selectAll("path.link").data(x.links(r)).enter().append("path").attr("class","link").attr("d",t);var v=s.selectAll("g.node").data(r).enter().append("g").attr("class","node").attr("transform",function(A){return"translate("+A.y+","+A.x+")"}).on("mouseover",function(B){var A=m.pluck(y.model.get_connected_nodes(B),"id");v.filter(function(C){return m.find(A,function(D){return D===C.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){v.style("fill","#000")});v.append("circle").attr("r",9);v.append("text").attr("dx",function(A){return A.children?-12:12}).attr("dy",3).attr("text-anchor",function(A){return A.children?"end":"start"}).text(function(A){return A.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(s){this.canvas_manager=new o.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var r=this;this.model.get("tracks").each(function(t){t.get("track").view=r});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var x=new k({model:this.model.get("parameter_tree")});$("#left").append(x.$el);var A=this,u=A.model.get("regions"),y=$("<tr/>").appendTo(this.track_collection_container);u.each(function(B){y.append($("<th>").text(B.toString()))});y.children().first().attr("colspan",2);var v=$("<div>").addClass("tiles");$("#right").append(v.append(this.track_collection_container));A.model.get("tracks").each(function(B){A.add_track(B)});var z=$(this.helpText).addClass("help"),w=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tooltip").remove();z.remove()}}]);z.prepend(w.$el.css("float","right"));$("#center").append(z);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var t=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var s=["Squish","Pack"],r={};m.each(s,function(B){r[B]=function(){A.model.set("default_mode",B);A.model.get("tracks").each(function(C){C.set("mode",B)})}});make_popupmenu(t.$el.find(".chevron-expand"),r);t.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(t.$el)},run_tool_on_dataset:function(s){var r=this.model.get("tool"),u=r.get("name"),t=this.model.get("dataset");r.set_input_values(s.get("values"));$.when(r.rerun(t)).then(function(v){});show_modal("Running "+u+" on complete dataset",u+" is running on dataset '"+t.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(u){var s=this,t=this.model.get("parameter_tree");s.model.add_track(u);var r=new l({model:u,canvas_manager:s.canvas_manager});r.on("run_on_dataset",s.run_tool_on_dataset,s);s.track_collection_container.append(r.$el);r.$el.hover(function(){var w=t.get_leaf(u.get("settings").get("values"));var v=m.pluck(t.get_connected_nodes(w),"id");q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(x){return m.find(v,function(y){return y===x.id})!==undefined}).style("fill","#f00")},function(){q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return u},handle_node_clicks:function(){var r=this,s=this.model.get("parameter_tree"),u=this.model.get("regions"),t=q.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");t.on("click",function(A,x){var w=r.model.get("tool"),z=r.model.get("dataset"),y=s.get_node_settings(A),v=$.Deferred();if(y.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+r.model.get("tool").get("name")+" with "+y.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();v.resolve(false)}})}else{v.resolve(true)}$.when(v).then(function(B){if(!B){return}var C=m.map(y,function(D){var E=new c({settings:D,regions:u,mode:r.model.get("default_mode")});r.add_track(E);return E});m.each(C,function(E,D){setTimeout(function(){w.set_input_values(E.get("settings").get("values"));$.when(w.rerun(z,u)).then(function(G){var H=G.first(),I=H.get("track_config");I.dataset=H;I.tool=null;var F=h.object_from_template(I,r,null);F.init_for_tool_data();F.prefs.block_color=r.block_color;F.prefs.reverse_strand_color=r.reverse_strand_color;E.set("track",F)})},D*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data","utils/config"],function(q,p,e,j,m,n,r,o){var k=Backbone.Model.extend({defaults:{inputs:null,values:null}});var a=Backbone.Model.extend({defaults:{tool:null,tree_data:null},initialize:function(t){var s=this;this.get("tool").get("inputs").each(function(u){u.on("change:min change:max change:num_samples",function(v){if(v.get("in_ptree")){s.set_tree_data()}},s);u.on("change:in_ptree",function(v){if(v.get("in_ptree")){s.add_param(v)}else{s.remove_param(v)}s.set_tree_data()},s)});if(t.config){q.each(t.config,function(v){var u=s.get("tool").get("inputs").find(function(w){return w.get("name")===v.name});s.add_param(u);u.set(v)})}},add_param:function(s){if(s.get("ptree_index")){return}s.set("in_ptree",true);s.set("ptree_index",this.get_tree_params().length)},remove_param:function(s){s.set("in_ptree",false);s.set("ptree_index",null);q(this.get_tree_params()).each(function(t,u){t.set("ptree_index",u+1)})},set_tree_data:function(){var t=q.map(this.get_tree_params(),function(v){return{param:v,samples:v.get_samples()}});var s=0,u=function(y,v){var A=y[v],z=A.param,x=z.get("label"),w=A.samples;if(y.length-1===v){return q.map(w,function(B){return{id:s++,name:B,param:z,value:B}})}return q.map(w,function(B){return{id:s++,name:B,param:z,value:B,children:u(y,v+1)}})};this.set("tree_data",{name:"Root",id:s++,children:(t.length!==0?u(t,0):null)})},get_tree_params:function(){return q(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(s){return s.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(s,t){return s*t.get_samples().length},1)},get_node_settings:function(w){var u=this.get("tool").get_inputs_dict();var x=w.parent;if(x){while(x.depth!==0){u[x.param.get("name")]=x.value;x=x.parent}}var s=this,t=function(z,y){if(z.param){y[z.param.get("name")]=z.value}if(!z.children){return new k({inputs:s.get("tool").get("inputs"),values:y})}else{return q.flatten(q.map(z.children,function(A){return t(A,q.clone(y))}))}},v=t(w,u);if(!q.isArray(v)){v=[v]}return v},get_connected_nodes:function(u){var v=function(w){if(!w.children){return w}else{return q.flatten([w,q.map(w.children,function(x){return v(x)})])}};var t=[],s=u.parent;while(s){t.push(s);s=s.parent}return q.flatten([t,v(u)])},get_leaf:function(t){var u=this.get("tree_data"),s=function(v){return q.find(v,function(w){return t[w.param.get("name")]===w.value})};while(u.children){u=s(u.children)}return u},toJSON:function(){return this.get_tree_params().map(function(s){return{name:s.get("name"),min:s.get("min"),max:s.get("max"),num_samples:s.get("num_samples")}})}});var d=Backbone.Model.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},initialize:function(s){this.set("regions",s.regions);if(s.track){var t=q.extend({data_url:galaxy_config.root+"dummy1",converted_datasets_state_url:galaxy_config.root+"dummy2"},s.track);this.set("track",m.object_from_template(t,{},null))}},same_settings:function(s){var t=this.get("settings"),u=s.get("settings");for(var v in t){if(!u[v]||t[v]!==u[v]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var l=Backbone.Collection.extend({model:d});var c=j.Visualization.extend({defaults:q.extend({},j.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),initialize:function(s){this.set("dataset",new r.Dataset(s.dataset));this.set("tool",new n.Tool(s.tool));this.set("regions",new j.GenomeRegionCollection(s.regions));this.set("tracks",new l(s.tracks));var t=this.get("tool");this.set("tool_with_samplable_inputs",t);t.remove_inputs(["data","hidden_data","conditional","text"]);this.set("parameter_tree",new a({tool:t,config:s.tree_config}))},add_track:function(s){this.get("tracks").add(s)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var h=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(s){this.canvas_manager=s.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var x=this.model.get("settings"),t=x.get("values"),v=$("<td/>").addClass("settings").appendTo(this.$el),u=$("<div/>").addClass("track-info").hide().appendTo(v);u.append($("<div/>").css("font-weight","bold").text("Track Settings"));x.get("inputs").each(function(z){u.append(z.get("label")+": "+t[z.get("name")]+"<br/>")});var s=this,y=$("<button/>").appendTo(u).text("Run on complete dataset").click(function(){u.toggle();s.trigger("run_on_dataset",x)});var w=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){u.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){s.$el.remove();$(".tooltip").remove()}}]);v.prepend(w.$el);this.model.get("regions").each(function(){s.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_config.root+"images/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var t=this,s=this.model.get("track"),v=this.model.get("regions"),u=this.$el.find("td.tile");if(!s){return}$.when(s.data_manager.data_is_ready()).then(function(w){v.each(function(z,y){var x=z.length()/t.TILE_LEN,B=1/x,A=t.model.get("mode");$.when(s.data_manager.get_data(z,A,x,{})).then(function(D){var C=t.canvas_manager.new_canvas();C.width=t.TILE_LEN;C.height=s.get_canvas_height(D,A,B,C.width);s.draw_tile(D,C.getContext("2d"),A,z,B);$(u[y]).empty().append(C)})})})}});var g=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(s){this.$el=s.tool_row;this.render()},render:function(){var t=this.model,x=t.get("type"),z=this.$el.find(".form-row-input"),v=null;z.find(":input").change(function(){t.set("value",$(this).val())});if(t instanceof n.IntegerToolParameter){v=$(q.template(this.number_input_template,this.model.toJSON()))}else{if(t instanceof n.SelectToolParameter){var u=q.map(this.$el.find("select option"),function(A){return $(A).val()}),w=u.join(", ");v=$(q.template(this.select_input_template,{options:w}))}}v.insertAfter(z);var s=this,y=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){t.set("in_ptree",true);z.hide();v.show();$(this).hide();s.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){t.set("in_ptree",false);v.hide();z.show();$(this).hide();s.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(y.$el);if(t.get("in_ptree")){z.hide();s.$el.find(".icon-button.plus-button").hide()}else{s.$el.find(".icon-button.toggle").hide();v.hide()}q.each(["min","max","num_samples"],function(A){v.find("."+A).change(function(){t.set(A,parseFloat($(this).val()))})})}});var i=Backbone.View.extend({className:"tree-design",initialize:function(s){this.render()},render:function(){var u=new n.ToolFormView({model:this.model.get("tool")});u.render();this.$el.append(u.$el);var t=this,s=t.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(v){var w=new g({model:s.at(v),tool_row:$(this)})})}});var b=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(s){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var A=this.model.get_tree_params();if(!A.length){return}this.width=100*(2+A.length);this.height=15*this.model.get_num_leaves();var z=this;var y=p.layout.cluster().size([this.height,this.width-160]);var u=p.svg.diagonal().projection(function(B){return[B.y,B.x]});var s=y.nodes(this.model.get("tree_data"));var v=q.uniq(q.pluck(s,"y"));q.each(A,function(D,C){var B=v[C+1],E=$("#center").position().left;z.$el.append($("<div>").addClass("label").text(D.get("label")).css("left",B+E))});var t=p.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var x=t.selectAll("path.link").data(y.links(s)).enter().append("path").attr("class","link").attr("d",u);var w=t.selectAll("g.node").data(s).enter().append("g").attr("class","node").attr("transform",function(B){return"translate("+B.y+","+B.x+")"}).on("mouseover",function(C){var B=q.pluck(z.model.get_connected_nodes(C),"id");w.filter(function(D){return q.find(B,function(E){return E===D.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){w.style("fill","#000")});w.append("circle").attr("r",9);w.append("text").attr("dx",function(B){return B.children?-12:12}).attr("dy",3).attr("text-anchor",function(B){return B.children?"end":"start"}).text(function(B){return B.name})}});var f=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(t){this.canvas_manager=new j.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new b({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var s=this;this.model.get("tracks").each(function(u){u.get("track").view=s});this.config=o.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},],{})},render:function(){var y=new i({model:this.model.get("parameter_tree")});$("#left").append(y.$el);var B=this,v=B.model.get("regions"),z=$("<tr/>").appendTo(this.track_collection_container);v.each(function(C){z.append($("<th>").text(C.toString()))});z.children().first().attr("colspan",2);var w=$("<div>").addClass("tiles");$("#right").append(w.append(this.track_collection_container));B.model.get("tracks").each(function(C){B.add_track(C)});var A=$(this.helpText).addClass("help"),x=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tooltip").remove();A.remove()}}]);A.prepend(x.$el.css("float","right"));$("#center").append(A);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var u=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var t=["Squish","Pack"],s={};q.each(t,function(C){s[C]=function(){B.model.set("default_mode",C);B.model.get("tracks").each(function(D){D.set("mode",C)})}});make_popupmenu(u.$el.find(".chevron-expand"),s);u.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(u.$el)},get_base_color:function(s){return this.config.get_value(s.toLowerCase()+"_color")||this.config.get_value("n_color")},run_tool_on_dataset:function(t){var s=this.model.get("tool"),v=s.get("name"),u=this.model.get("dataset");s.set_input_values(t.get("values"));$.when(s.rerun(u)).then(function(w){});show_modal("Running "+v+" on complete dataset",v+" is running on dataset '"+u.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(v){var t=this,u=this.model.get("parameter_tree");t.model.add_track(v);var s=new h({model:v,canvas_manager:t.canvas_manager});s.on("run_on_dataset",t.run_tool_on_dataset,t);t.track_collection_container.append(s.$el);s.$el.hover(function(){var x=u.get_leaf(v.get("settings").get("values"));var w=q.pluck(u.get_connected_nodes(x),"id");p.select(t.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(y){return q.find(w,function(z){return z===y.id})!==undefined}).style("fill","#f00")},function(){p.select(t.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return v},handle_node_clicks:function(){var s=this,t=this.model.get("parameter_tree"),v=this.model.get("regions"),u=p.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");u.on("click",function(B,y){var x=s.model.get("tool"),A=s.model.get("dataset"),z=t.get_node_settings(B),w=$.Deferred();if(z.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+s.model.get("tool").get("name")+" with "+z.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();w.resolve(false)}})}else{w.resolve(true)}$.when(w).then(function(C){if(!C){return}var D=q.map(z,function(E){var F=new d({settings:E,regions:v,mode:s.model.get("default_mode")});s.add_track(F);return F});q.each(D,function(F,E){setTimeout(function(){x.set_input_values(F.get("settings").get("values"));$.when(x.rerun(A,v)).then(function(H){var I=H.first(),J=I.get("track_config");J.dataset=I;J.tool=null;J.prefs=s.config.to_key_value_dict();var G=m.object_from_template(J,s,null);G.init_for_tool_data();F.set("track",G)})},E*10000)})})})}});return{SweepsterVisualization:c,SweepsterVisualizationView:f}}); \ No newline at end of file diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -304,6 +304,7 @@ }); return { + ConfigSetting: ConfigSetting, ConfigSettingCollection: ConfigSettingCollection, ConfigSettingCollectionView: ConfigSettingCollectionView }; diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -3,8 +3,8 @@ * genomic visualization. */ -define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], - function(_, d3, util, visualization, tracks, tools, data) { +define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data", "utils/config"], + function(_, d3, util, visualization, tracks, tools, data, config) { /** * A collection of tool input settings. Object is useful for keeping a list of settings @@ -257,7 +257,7 @@ }, initialize: function(options) { - this.set('regions', new visualization.GenomeRegionCollection(options.regions)); + this.set('regions', options.regions); if (options.track) { // FIXME: find a better way to deal with needed URLs: var track_config = _.extend({ @@ -310,12 +310,12 @@ this.set('dataset', new data.Dataset(options.dataset)); this.set('tool', new tools.Tool(options.tool)); this.set('regions', new visualization.GenomeRegionCollection(options.regions)); - this.set('tracks', new SweepsterTrackCollection(options.tracks)); + this.set('tracks', new TrackCollection(options.tracks)); var tool_with_samplable_inputs = this.get('tool'); this.set('tool_with_samplable_inputs', tool_with_samplable_inputs); // Remove complex parameters for now. - tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional' ] ); + tool_with_samplable_inputs.remove_inputs( [ 'data', 'hidden_data', 'conditional', 'text' ] ); this.set('parameter_tree', new ToolParameterTree({ tool: tool_with_samplable_inputs, @@ -430,7 +430,7 @@ var canvas = self.canvas_manager.new_canvas(); canvas.width = self.TILE_LEN; canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width); - track.draw_tile(tile_data, canvas.getContext('2d'), mode, resolution, region, w_scale); + track.draw_tile(tile_data, canvas.getContext('2d'), mode, region, w_scale); $(tile_containers[index]).empty().append(canvas); }); }); @@ -680,8 +680,18 @@ }); // Set block, reverse strand block colors; these colors will be used for all tracks. - this.block_color = util.get_random_color(); - this.reverse_strand_color = util.get_random_color( [ this.block_color, "#ffffff" ] ); + this.config = config.ConfigSettingCollection.from_models_and_saved_values( + [ + { key: 'name', label: 'Name', type: 'text', default_value: '' }, + { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, + { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" }, + { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" }, + { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" }, + { key: 'n_color', label: 'N Color', type: 'color', default_value: "#AAAAAA" }, + { key: 'block_color', label: 'Block color', type: 'color' }, + { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' }, + ], {} + ); }, render: function() { @@ -792,6 +802,11 @@ $("#right .unified-panel-header-inner").append(menu.$el); }, + get_base_color: function(base) { + return this.config.get_value(base.toLowerCase() + '_color') || + this.config.get_value('n_color'); + }, + run_tool_on_dataset: function(settings) { var tool = this.model.get('tool'), tool_name = tool.get('name'), @@ -904,14 +919,12 @@ // the tool parameters and parameter tree. track_config.tool = null; + track_config.prefs = self.config.to_key_value_dict(); + // Create and add track for output dataset. var track_obj = tracks.object_from_template(track_config, self, null); track_obj.init_for_tool_data(); - // Set track block colors. - track_obj.prefs.block_color = self.block_color; - track_obj.prefs.reverse_strand_color = self.reverse_strand_color; - pm_track.set('track', track_obj); }); }, index * 10000); diff -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 -r 5d666f5fae293488bc4f934125778f67627bc1e5 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2243,7 +2243,7 @@ on_click_fn: function(track) { var template = '<strong>Tool</strong>: <%= track.tool.get("name") %><br/>' + - '<strong>Dataset</strong>: <%= track.config.get("name") %><br/>' + + '<strong>Dataset</strong>: <%= track.config.get_value("name") %><br/>' + '<strong>Region(s)</strong>: <select name="regions">' + '<option value="cur">current viewing area</option>' + '<option value="bookmarks">bookmarks</option>' + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e20408b06d65/ Changeset: e20408b06d65 User: greg Date: 2014-04-10 23:11:01 Summary: Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids. Affected #: 27 files diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -16,6 +16,7 @@ from tool_shed.util import data_manager_util from tool_shed.util import datatype_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util @@ -1851,7 +1852,7 @@ repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) ) else: repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) - repo = hg.repository( suc.get_configured_ui(), path=repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), path=repo_files_dir ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) suc.update_repository( repo, latest_ctx_rev ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -13,6 +13,7 @@ import tool_shed.util.shed_util_common as suc from tool_shed.galaxy_install import repository_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util @@ -49,7 +50,7 @@ log.debug( error_message ) return [] repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) return ordered_installable_revisions else: @@ -133,7 +134,7 @@ # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -6,6 +6,7 @@ from galaxy.model.orm import and_, not_, select from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest from tool_shed.util import export_util +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc from galaxy import eggs @@ -168,7 +169,7 @@ # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository_dependency.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency, repo, changeset_revision ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -19,6 +19,7 @@ from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import export_util +from tool_shed.util import hg_util from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import readme_util @@ -719,7 +720,7 @@ status = kwd.get( 'status', 'done' ) commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. suc.update_repository( repo ) changeset_revision = repository.tip( trans.app ) @@ -891,9 +892,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Default to the current changeset revision. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) latest_changeset_revision = changeset_revision from_update_manager = kwd.get( 'from_update_manager', False ) if from_update_manager: @@ -937,10 +938,10 @@ update_to_changeset_hash = None for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: if changeset_hash == repository.tip( trans.app ): - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash break else: @@ -949,7 +950,7 @@ changeset_hash ) if repository_metadata: # We found a RepositoryMetadata record. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash break else: @@ -1213,7 +1214,7 @@ else: containers_dict = None export_repository_dependencies_check_box = None - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return trans.fill_template( "/webapps/tool_shed/repository/export_repository.mako", changeset_revision=changeset_revision, containers_dict=containers_dict, @@ -1466,9 +1467,9 @@ has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ] repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) ctx_rev = str( update_to_ctx.rev() ) latest_changeset_revision = changeset_revision update_dict = dict( changeset_revision=changeset_revision, @@ -1497,7 +1498,7 @@ has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False changeset_hash = str( repo.changectx( changeset ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), @@ -1515,10 +1516,10 @@ # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash else: - update_to_ctx = suc.get_changectx_for_changeset( repo, update_to_changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, update_to_changeset_hash ) latest_changeset_revision = update_to_changeset_hash break elif not update_to_changeset_hash and changeset_hash == changeset_revision: @@ -1544,8 +1545,8 @@ changeset_revision = kwd[ 'changeset_revision' ] repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) if ctx: return str( ctx.rev() ) return '' @@ -1560,8 +1561,8 @@ def get_file_from_changeset_revision( self, repo_files_dir, changeset_revision, file_name, dir ): """Return file_name from the received changeset_revision of the repository manifest.""" stripped_file_name = suc.strip_path( file_name ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir ) return named_tmp_file @@ -1604,7 +1605,7 @@ trans.model.Repository.table.c.user_id == user.id ) ): repository = repository_metadata.repository repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) latest_downloadable_changeset_revsion = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) if repository_metadata.changeset_revision == latest_downloadable_changeset_revsion: # We'll display only the test run for the latest installable revision in the rss feed. @@ -1672,7 +1673,7 @@ if repository_name is not None and repository_owner is not None: repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) if repository: - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) return suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) return suc.INITIAL_CHANGELOG_HASH @@ -1855,7 +1856,7 @@ changeset_revision = kwd[ 'changeset_revision' ] repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) tool_version_dicts = [] for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) @@ -1880,7 +1881,7 @@ repository_id = trans.security.encode_id( repository.id ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if not repository_metadata: # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository @@ -1889,7 +1890,7 @@ repo, after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = repository_util.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, @@ -2165,7 +2166,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) repository_type = kwd.get( 'repository_type', str( repository.type ) ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repo_name = kwd.get( 'repo_name', repository.name ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) description = kwd.get( 'description', repository.description ) @@ -2317,7 +2318,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False ) repository_metadata = None metadata = None is_malicious = False @@ -2326,7 +2327,7 @@ if changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious else: @@ -2337,7 +2338,7 @@ if previous_changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision ) if repository_metadata: - revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious changeset_revision = previous_changeset_revision @@ -2443,7 +2444,7 @@ # There is no repository_metadata defined for the changeset_revision, so see if it was defined # in a previous changeset in the changelog. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) previous_changeset_revision = \ suc.get_previous_metadata_changeset_revision( repository, repo, @@ -2520,7 +2521,7 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the next installable changeset_revision beyond the received changeset_revision. changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if changeset_revision: @@ -2540,7 +2541,7 @@ status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: @@ -2577,7 +2578,7 @@ repository_metadata_id = None metadata = None repository_dependencies = None - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, @@ -2607,7 +2608,7 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the lower bound changeset revision. lower_bound_changeset_revision = suc.get_previous_metadata_changeset_revision( repository, repo, changeset_revision, downloadable=True ) # Build the list of changeset revision hashes. @@ -2633,7 +2634,7 @@ status='error' ) ) repository = suc.get_repository_in_tool_shed( trans, id ) changeset_revision = repository.tip( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -2651,7 +2652,7 @@ changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, @@ -2702,7 +2703,7 @@ commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' ) if kwd.get( 'select_files_to_delete_button', False ): if selected_files_to_delete: @@ -2742,7 +2743,7 @@ # Update the repository files for browsing. suc.update_repository( repo ) # Get the new repository tip. - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) if tip == repository.tip( trans.app ): message += 'No changes to repository. ' kwd[ 'message' ] = message @@ -2931,7 +2932,7 @@ if not repository_metadata: # Get updates to the received changeset_revision if any exist. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if upper_bound_changeset_revision: changeset_revision = upper_bound_changeset_revision @@ -2971,7 +2972,7 @@ trans.security.encode_id( repository.id ), changeset_revision ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) tool_shed_status_dict = {} # Handle repository deprecation. tool_shed_status_dict[ 'repository_deprecated' ] = str( repository.deprecated ) @@ -3063,7 +3064,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) changesets = [] for changeset in repo.changelog: ctx = repo.changectx( changeset ) @@ -3074,7 +3075,7 @@ change_dict = { 'ctx' : ctx, 'rev' : str( ctx.rev() ), 'date' : date, - 'display_date' : suc.get_readable_ctx_date( ctx ), + 'display_date' : hg_util.get_readable_ctx_date( ctx ), 'description' : ctx.description(), 'files' : ctx.files(), 'user' : ctx.user(), @@ -3098,8 +3099,8 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, ctx_str ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = hg_util.get_changectx_for_changeset( repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' @@ -3129,7 +3130,7 @@ metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: - ctx_parent_date = suc.get_readable_ctx_date( ctx_parent ) + ctx_parent_date = hg_util.get_readable_ctx_date( ctx_parent ) ctx_parent_rev = ctx_parent.rev() if ctx_parent_rev < 0: prev = None @@ -3138,7 +3139,7 @@ else: prev = None if ctx_child: - ctx_child_date = suc.get_readable_ctx_date( ctx_child ) + ctx_child_date = hg_util.get_readable_ctx_date( ctx_child ) ctx_child_rev = ctx_child.rev() next = "<b>%s:%s</b><i>(%s)</i>" % ( ctx_child_rev, ctx_child, ctx_child_date ) else: @@ -3187,7 +3188,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) display_reviews = kwd.get( 'display_reviews', False ) @@ -3221,7 +3222,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -3277,13 +3278,13 @@ render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) tool_metadata_dict = {} tool_lineage = [] tool = None guid = None original_tool_data_path = trans.app.config.tool_data_path - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -7,6 +7,7 @@ from galaxy.webapps.tool_shed.util import ratings_util from tool_shed.util.container_util import STRSEP import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import review_util from galaxy.util.odict import odict import tool_shed.grids.repository_review_grids as repository_review_grids @@ -72,8 +73,8 @@ status = kwd.get( 'status', 'done' ) review = review_util.get_review( trans, kwd[ 'id' ] ) repository = review.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako', repository=repository, changeset_revision_label=changeset_revision_label, @@ -232,7 +233,7 @@ for component in review_util.get_components( trans ): components_dict[ component.name ] = dict( component=component, component_review=None ) repository = review.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) for component_review in review.component_reviews: if component_review and component_review.component: component_name = component_review.component.name @@ -337,7 +338,7 @@ name='revision_approved', selected_value=selected_value, for_component=False ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako', repository=repository, review=review, @@ -470,7 +471,7 @@ if repository_id: repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] reviews_dict = odict() @@ -478,7 +479,7 @@ ctx = repo.changectx( changeset ) changeset_revision = str( ctx ) if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes: - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) if changeset_revision in reviewed_revision_hashes: # Find the review for this changeset_revision repository_reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) @@ -517,9 +518,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako', repository=repository, @@ -582,9 +583,9 @@ status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) previous_reviews_dict = review_util.get_previous_repository_reviews( trans, repository, changeset_revision ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako', repository=repository, changeset_revision=changeset_revision, diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -11,6 +11,7 @@ import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc from tool_shed.util import commit_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_dependency_util from tool_shed.util import tool_dependency_util @@ -39,7 +40,7 @@ repository_id = kwd.get( 'repository_id', '' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) ) remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None @@ -63,7 +64,7 @@ repo_url = 'http%s' % url[ len( 'hg' ): ] repo_url = repo_url.encode( 'ascii', 'replace' ) try: - commands.clone( suc.get_configured_ui(), repo_url, uploaded_directory ) + commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory ) except Exception, e: message = 'Error uploading via mercurial clone: %s' % suc.to_html_string( str( e ) ) status = 'error' @@ -323,7 +324,7 @@ def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 if upload_point is not None: @@ -387,7 +388,7 @@ def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 ok, message = commit_util.check_archive( repository, tar ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -15,6 +15,7 @@ from tool_shed.util import data_manager_util from tool_shed.util import datatype_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import repository_dependency_util from tool_shed.util import metadata_util from tool_shed.util import tool_dependency_util @@ -186,7 +187,7 @@ def get_repo_info_dict( trans, repository_id, changeset_revision ): repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, @@ -225,7 +226,7 @@ has_repository_dependencies_only_if_compiling_contained_td = False includes_tool_dependencies = False includes_tools_for_display_in_tool_panel = False - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, @@ -574,7 +575,7 @@ current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_ctx_rev != ctx_rev: - repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) + repo = hg.repository( hg_util.get_configured_ui(), path=os.path.abspath( install_dir ) ) pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) handle_repository_contents( trans, @@ -804,7 +805,7 @@ def pull_repository( repo, repository_clone_url, ctx_rev ): """Pull changes from a remote repository to a local one.""" - commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) + commands.pull( hg_util.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) def repair_tool_shed_repository( trans, repository, repo_info_dict ): diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -5,6 +5,7 @@ from galaxy.webapps.tool_shed import model from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.grids.repository_grids import CategoryGrid from tool_shed.grids.repository_grids import RepositoryGrid @@ -425,9 +426,11 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - return suc.get_revision_label( trans, repository, repository_metadata.changeset_revision, include_date=True ) + return hg_util.get_revision_label( trans, + repository, + repository_metadata.changeset_revision, + include_date=True, + include_hash=True ) class ToolsColumn( grids.TextColumn ): diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -6,6 +6,7 @@ from galaxy.model.orm import or_ from galaxy.util import json from galaxy.util import listify +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc import tool_shed.grids.util as grids_util import tool_shed.repository_types.util as rt_util @@ -116,7 +117,7 @@ def get_value( self, trans, grid, repository ): """Display the current repository heads.""" repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) heads = suc.get_repository_heads( repo ) multiple_heads = len( heads ) > 1 if multiple_heads: @@ -124,7 +125,7 @@ else: heads_str = '' for ctx in heads: - heads_str += '%s<br/>' % suc.get_revision_label_from_ctx( ctx, include_date=True ) + heads_str += '%s<br/>' % hg_util.get_revision_label_from_ctx( ctx, include_date=True ) heads_str.rstrip( '<br/>' ) if multiple_heads: heads_str += '</font>' @@ -1338,7 +1339,7 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository changeset_revision = repository_metadata.changeset_revision - changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + changeset_revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return changeset_revision_label @@ -1482,7 +1483,7 @@ changeset_revision ) if not required_repository_metadata: repo_dir = required_repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) updated_changeset_revision = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset_revision ) required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, @@ -2029,7 +2030,7 @@ tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) repository_metadata = None try: @@ -2077,7 +2078,7 @@ tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) try: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -6,6 +6,7 @@ from galaxy.model.orm import or_ from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import metadata_util from galaxy import eggs @@ -66,10 +67,10 @@ # Restrict to revisions that have been reviewed. if repository.reviews: rval = '' - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) for review in repository.reviews: changeset_revision = review.changeset_revision - rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \ ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval @@ -85,9 +86,11 @@ rval = '' for repository_metadata in repository_metadata_revisions: rev, label, changeset_revision = \ - metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository, + include_date=True, + include_hash=False ) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \ ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval @@ -308,7 +311,11 @@ rval += 'edit_review' else: rval +='browse_review' - revision_label = suc.get_revision_label( trans, review.repository, review.changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, + review.repository, + review.changeset_revision, + include_date=True, + include_hash=False ) rval += '?id=%s">%s</a>' % ( encoded_review_id, revision_label ) return rval diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -1,7 +1,7 @@ import logging import os import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util +from tool_shed.util import hg_util from galaxy.web.form_builder import SelectField from galaxy.util.bunch import Bunch @@ -96,9 +96,11 @@ repository_metadata_revisions = repository.metadata_revisions for repository_metadata in repository_metadata_revisions: rev, label, changeset_revision = \ - metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + hg_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository, + include_date=True, + include_hash=False ) changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -14,6 +14,7 @@ import ConfigParser import galaxy.webapps.tool_shed.config as tool_shed_config +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc import logging import shutil @@ -109,7 +110,7 @@ if tool_dicts is not None: # Clone the repository up to the changeset revision we're checking. repo_dir = repository.repo_path( app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cafr" ) cloned_ok, error_message = suc.clone_repository( repo_dir, work_dir, changeset_revision ) if cloned_ok: @@ -368,7 +369,7 @@ """ if not testable_revision: repo_dir = repository.repo_path( app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) if len( changeset_revisions ) > 1: latest_downloadable_revision = changeset_revisions[ -1 ] diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -12,6 +12,7 @@ from galaxy.util.odict import odict from galaxy.web import url_for import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import tool_util from tool_shed.util import xml_util import tool_shed.repository_types.util as rt_util @@ -156,7 +157,7 @@ def handle_directory_changes( trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) content_alert_str = '' files_to_remove = [] filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ] @@ -342,7 +343,7 @@ repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if repository: repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) lastest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) if lastest_installable_changeset_revision != suc.INITIAL_CHANGELOG_HASH: elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -14,6 +14,7 @@ from tool_shed.util import common_install_util from tool_shed.util import common_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import repository_dependency_util from tool_shed.util import xml_util @@ -37,7 +38,7 @@ def archive_repository_revision( trans, ui, repository, archive_dir, changeset_revision ): '''Create an un-versioned archive of a repository.''' - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) options_dict = suc.get_mercurial_default_options_dict( 'archive' ) options_dict[ 'rev' ] = changeset_revision error_message = '' @@ -233,8 +234,8 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = {} # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/hg_util.py --- /dev/null +++ b/lib/tool_shed/util/hg_util.py @@ -0,0 +1,108 @@ +import logging +from datetime import datetime +from time import gmtime +from time import strftime + +from galaxy import eggs +eggs.require( 'mercurial' ) + +from mercurial import cmdutil +from mercurial import commands +from mercurial import hg +from mercurial import ui + +def get_changectx_for_changeset( repo, changeset_revision, **kwd ): + """Retrieve a specified changectx from a repository.""" + for changeset in repo.changelog: + ctx = repo.changectx( changeset ) + if str( ctx ) == changeset_revision: + return ctx + return None + +def get_configured_ui(): + """Configure any desired ui settings.""" + _ui = ui.ui() + # The following will suppress all messages. This is + # the same as adding the following setting to the repo + # hgrc file' [ui] section: + # quiet = True + _ui.setconfig( 'ui', 'quiet', True ) + return _ui + +def get_readable_ctx_date( ctx ): + """Convert the date of the changeset (the received ctx) to a human-readable date.""" + t, tz = ctx.date() + date = datetime( *gmtime( float( t ) - tz )[ :6 ] ) + ctx_date = date.strftime( "%Y-%m-%d" ) + return ctx_date + +def get_revision_label( trans, repository, changeset_revision, include_date=True, include_hash=True ): + """ + Return a string consisting of the human read-able changeset rev and the changeset revision string + which includes the revision date if the receive include_date is True. + """ + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + return get_revision_label_from_ctx( ctx, include_date=include_date, include_hash=include_hash ) + else: + if include_hash: + return "-1:%s" % changeset_revision + else: + return "-1" + +def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None, + include_date=True, include_hash=True ): + if repository is None: + repository = repository_metadata.repository + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + if include_date: + changeset_revision_date = get_readable_ctx_date( ctx ) + if include_hash: + label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date ) + else: + label = "%s (%s)" % ( str( ctx.rev() ), changeset_revision_date ) + else: + if include_hash: + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + label = "%s" % str( ctx.rev() ) + else: + rev = '-1' + if include_hash: + label = "-1:%s" % changeset_revision + else: + label = "-1" + return rev, label, changeset_revision + +def get_revision_label_from_ctx( ctx, include_date=True, include_hash=True ): + if include_date: + if include_hash: + return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) ) + else: + return '%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), str( get_readable_ctx_date( ctx ) ) ) + else: + if include_hash: + return '%s:%s' % ( str( ctx.rev() ), str( ctx ) ) + else: + return '%s' % str( ctx.rev() ) + +def get_rev_label_from_changeset_revision( repo, changeset_revision, include_date=True, include_hash=True ): + """ + Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash + which includes the revision date if the receive include_date is True. + """ + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = get_revision_label_from_ctx( ctx, include_date=include_date ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + return rev, label diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -8,6 +8,7 @@ from galaxy.datatypes import checkers from tool_shed.util import commit_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc @@ -212,7 +213,7 @@ archive_file_path = os.path.join( file_path, archive_file_name ) archive = tarfile.open( archive_file_path, 'r:*' ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 ok, error_message = commit_util.check_archive( repository, archive ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -15,6 +15,7 @@ from tool_shed.util import common_util from tool_shed.util import common_install_util from tool_shed.util import container_util +from tool_shed.util import hg_util from tool_shed.util import readme_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util @@ -347,7 +348,7 @@ # changeset revision in the received repository's changelog (up to the received changeset revision) to see if it is contained in the # skip_tool_test table. If it is, but is not associated with a repository_metadata record, reset that skip_tool_test record to the # newly created repository_metadata record. - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) skip_tool_test = suc.get_skip_tool_test_by_changeset_revision( trans, changeset_hash ) @@ -1048,7 +1049,7 @@ def get_latest_repository_metadata( trans, decoded_repository_id, downloadable=False ): """Get last metadata defined for a specified repository from the database.""" repository = trans.sa_session.query( trans.model.Repository ).get( decoded_repository_id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) if downloadable: changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) else: @@ -1121,21 +1122,6 @@ repository_metadata_revisions.append( metadata_revision ) return repository_metadata_revisions -def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ): - if repository is None: - repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - changeset_revision = repository_metadata.changeset_revision - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - changeset_revision_date = suc.get_readable_ctx_date( ctx ) - rev = '%04d' % ctx.rev() - label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - return rev, label, changeset_revision - def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: @@ -1294,7 +1280,7 @@ log.debug( error_message ) is_valid = False return repository_dependency_tup, is_valid, error_message - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( app ) ) # The received changeset_revision may be None since defining it in the dependency definition is optional. # If this is the case, the default will be to set it's value to the repository dependency tip revision. # This probably occurs only when handling circular dependency definitions. @@ -1360,7 +1346,7 @@ """ if repository.deleted: return ( None, False ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) # Get the latest installable changeset revision since that is all that is currently configured for testing. latest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) if latest_installable_changeset_revision not in [ None, suc.INITIAL_CHANGELOG_HASH ]: @@ -1797,7 +1783,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. @@ -1978,7 +1964,7 @@ encoded_id = trans.security.encode_id( repository.id ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, changeset_revision=repository.tip( trans.app ), diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -9,6 +9,7 @@ from galaxy.util import unicodify import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util +from tool_shed.util import hg_util eggs.require( 'mercurial' ) @@ -25,7 +26,7 @@ if trans.webapp.name == 'galaxy': can_use_disk_files = True else: - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision readme_files_dict = {} @@ -74,7 +75,7 @@ readme_files_dict[ readme_file_name ] = text_of_reasonable_length else: # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest. - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) if ctx: fctx = suc.get_file_context_from_ctx( ctx, readme_file_name ) if fctx and fctx not in [ 'DELETED' ]: diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -9,6 +9,7 @@ from tool_shed.util import common_install_util from tool_shed.util import container_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import tool_util @@ -532,7 +533,7 @@ else: # The repository changeset_revision is no longer installable, so see if there's been an update. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision ) repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, trans.security.encode_id( repository.id ), diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -3,6 +3,7 @@ import os import re import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import import_util from galaxy import util from galaxy.web.form_builder import build_select_field @@ -47,7 +48,7 @@ # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. The hg # purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll remove unknown files # and empty directories. This is not currently used because it is not supported in the mercurial API. - repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), path=repository.repo_path( trans.app ) ) fp = repo.opener( 'hgrc', 'wb' ) fp.write( '[paths]\n' ) fp.write( 'default = .\n' ) @@ -83,7 +84,7 @@ if not os.path.exists( repository_path ): os.makedirs( repository_path ) # Create the local repository. - repo = hg.repository( suc.get_configured_ui(), repository_path, create=True ) + repo = hg.repository( hg_util.get_configured_ui(), repository_path, create=True ) # Add an entry in the hgweb.config file for the local repository. lhs = "repos/%s/%s" % ( repository.user.username, repository.name ) trans.app.hgweb_config_manager.add_entry( lhs, repository_path ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/review_util.py --- a/lib/tool_shed/util/review_util.py +++ b/lib/tool_shed/util/review_util.py @@ -3,6 +3,7 @@ from galaxy import eggs from galaxy.model.orm import and_ from galaxy.util.odict import odict +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc eggs.require( 'mercurial' ) @@ -58,13 +59,13 @@ def get_previous_repository_reviews( trans, repository, changeset_revision ): """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] previous_reviews_dict = odict() for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) if previous_changeset_revision in reviewed_revision_hashes: - previous_rev, previous_changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) + previous_rev, previous_changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, trans.security.encode_id( repository.id ), previous_changeset_revision ) @@ -93,7 +94,7 @@ def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -4,9 +4,6 @@ import shutil import string import tempfile -from datetime import datetime -from time import gmtime -from time import strftime from galaxy import util from galaxy.util import asbool from galaxy.util import json @@ -19,6 +16,7 @@ import sqlalchemy.orm.exc from tool_shed.util import common_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import xml_util import tool_shed.repository_types.util as rt_util from xml.etree import ElementTree as XmlET @@ -143,7 +141,7 @@ def changeset_is_valid( app, repository, changeset_revision ): """Make sure a changeset hash is valid for a specified repository.""" - repo = hg.repository( get_configured_ui(), repository.repo_path( app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( app ) ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) if changeset_revision == changeset_hash: @@ -167,7 +165,7 @@ def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" try: - commands.clone( get_configured_ui(), + commands.clone( hg_util.get_configured_ui(), str( repository_clone_url ), dest=str( repository_file_dir ), pull=True, @@ -469,14 +467,6 @@ except sqlalchemy.orm.exc.NoResultFound: return None -def get_changectx_for_changeset( repo, changeset_revision, **kwd ): - """Retrieve a specified changectx from a repository.""" - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == changeset_revision: - return ctx - return None - def get_config( config_file, repo, ctx, dir ): """Return the latest version of config_filename from the repository manifest.""" config_file = strip_path( config_file ) @@ -496,16 +486,6 @@ return os.path.abspath( os.path.join( root, name ) ) return None -def get_configured_ui(): - """Configure any desired ui settings.""" - _ui = ui.ui() - # The following will suppress all messages. This is - # the same as adding the following setting to the repo - # hgrc file' [ui] section: - # quiet = True - _ui.setconfig( 'ui', 'quiet', True ) - return _ui - def get_ctx_rev( app, tool_shed_url, name, owner, changeset_revision ): """ Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the @@ -539,7 +519,7 @@ if repository_metadata: return repository_metadata # The installable changeset_revision may have been changed because it was "moved ahead" in the repository changelog. - repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) updated_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision=changeset_revision ) if updated_changeset_revision: repository_metadata = get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, updated_changeset_revision ) @@ -590,7 +570,7 @@ # record, so updates must be necessary. defined_repository = get_repository_by_name_and_owner( trans.app, name, owner ) defined_repo_dir = defined_repository.repo_path( trans.app ) - defined_repo = hg.repository( get_configured_ui(), defined_repo_dir ) + defined_repo = hg.repository( hg_util.get_configured_ui(), defined_repo_dir ) updated_changeset_revision = \ get_next_downloadable_changeset_revision( defined_repository, defined_repo, @@ -799,7 +779,7 @@ changeset_tups = [] for repository_metadata in metadata_revisions: changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() else: @@ -913,13 +893,6 @@ return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) -def get_readable_ctx_date( ctx ): - """Convert the date of the changeset (the received ctx) to a human-readable date.""" - t, tz = ctx.date() - date = datetime( *gmtime( float( t ) - tz )[ :6 ] ) - ctx_date = date.strftime( "%Y-%m-%d" ) - return ctx_date - def get_repo_info_tuple_contents( repo_info_tuple ): """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: @@ -1211,38 +1184,6 @@ reversed_changelog.insert( 0, changeset ) return reversed_changelog -def get_revision_label( trans, repository, changeset_revision, include_date=True ): - """ - Return a string consisting of the human read-able changeset rev and the changeset revision string - which includes the revision date if the receive include_date is True. - """ - repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - return get_revision_label_from_ctx( ctx, include_date=include_date ) - else: - return "-1:%s" % changeset_revision - -def get_revision_label_from_ctx( ctx, include_date=True ): - if include_date: - return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ - ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) ) - return '%s:%s' % ( str( ctx.rev() ), str( ctx ) ) - -def get_rev_label_from_changeset_revision( repo, changeset_revision, include_date=True ): - """ - Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash - which includes the revision date if the receive include_date is True. - """ - ctx = get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - rev = '%04d' % ctx.rev() - label = get_revision_label_from_ctx( ctx, include_date=include_date ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - return rev, label - def get_shed_tool_conf_dict( app, shed_tool_conf ): """Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict associated with the file.""" for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ): @@ -1434,7 +1375,7 @@ """ repository = get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the upper bound changeset revision. upper_bound_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) # Build the list of changeset revision hashes defining each available update up to, but excluding, upper_bound_changeset_revision. @@ -1487,7 +1428,7 @@ that was included in the change set. """ repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) sharable_link = generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None ) smtp_server = trans.app.config.smtp_server if smtp_server and ( new_repo_alert or repository.email_alerts ): @@ -1510,7 +1451,7 @@ template = new_repo_email_alert_template else: template = email_alert_template - display_date = get_readable_ctx_date( ctx ) + display_date = hg_util.get_readable_ctx_date( ctx ) admin_body = string.Template( template ).safe_substitute( host=trans.request.host, sharable_link=sharable_link, repository_name=repository.name, @@ -1859,7 +1800,7 @@ # I = ignored # It would be nice if we could use mercurial's purge extension to remove untracked files. The problem is that # purging is not supported by the mercurial API. - commands.update( get_configured_ui(), repo, rev=ctx_rev ) + commands.update( hg_util.get_configured_ui(), repo, rev=ctx_rev ) def update_tool_shed_repository_status( app, tool_shed_repository, status, error_message=None ): """Update the status of a tool shed repository in the process of being installed into Galaxy.""" diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -15,6 +15,7 @@ from galaxy.web.form_builder import SelectField from galaxy.tools.actions.upload import UploadToolAction from tool_shed.util import common_util +from tool_shed.util import hg_util from tool_shed.util import xml_util import tool_shed.util.shed_util_common as suc from xml.etree import ElementTree as XmlET @@ -538,7 +539,7 @@ """ repository = suc.get_repository_by_id( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Initialize the tool lineage version_lineage = [ guid ] # Get all ancestor guids of the received guid. @@ -637,7 +638,7 @@ def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, repository_id, changeset_revision, tool_config_filename, work_dir ): tool = None message = '' - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) # We're not currently doing anything with the returned list of deleted_sample_files here. It is intended to help handle sample files that are in # the manifest, but have been deleted from disk. sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) @@ -866,7 +867,7 @@ original_tool_data_path = trans.app.config.tool_data_path repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) message = '' tool = None can_use_disk_file = False diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 templates/webapps/tool_shed/common/common.mako --- a/templates/webapps/tool_shed/common/common.mako +++ b/templates/webapps/tool_shed/common/common.mako @@ -107,7 +107,7 @@ <%def name="render_multiple_heads_message( heads )"><div class="warningmessage"><% - from tool_shed.util.shed_util_common import get_revision_label_from_ctx + from tool_shed.util.hg_util import get_revision_label_from_ctx heads_str = '' for ctx in heads: heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 templates/webapps/tool_shed/repository/view_changeset.mako --- a/templates/webapps/tool_shed/repository/view_changeset.mako +++ b/templates/webapps/tool_shed/repository/view_changeset.mako @@ -49,7 +49,7 @@ %endif <div class="toolForm"><% - from tool_shed.util.shed_util_common import get_readable_ctx_date + from tool_shed.util.hg_util import get_readable_ctx_date changeset_revision_date = get_readable_ctx_date( ctx ) if can_download: title_str = 'Changeset <b>%s:%s</b><i>(%s)</i>' % ( ctx.rev(), ctx, changeset_revision_date ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1418,10 +1418,10 @@ def verify_repository_reviews( self, repository, reviewer=None, strings_displayed=[], strings_not_displayed=[] ): changeset_revision = self.get_repository_tip( repository ) # Verify that the currently logged in user has a repository review for the specified repository, reviewer, and changeset revision. - strings_displayed=[ repository.name, reviewer.username, changeset_revision ] + strings_displayed=[ repository.name, reviewer.username ] self.display_reviewed_repositories_owned_by_user( strings_displayed=strings_displayed ) # Verify that the reviewer has reviewed the specified repository's changeset revision. - strings_displayed=[ repository.name, repository.description, changeset_revision ] + strings_displayed=[ repository.name, repository.description ] self.display_repository_reviews_by_user( reviewer, strings_displayed=strings_displayed ) # Load the review and check for the components passed in strings_displayed. review = test_db_util.get_repository_review_by_user_id_changeset_revision( reviewer.id, repository.id, changeset_revision ) diff -r 452af6869205b773d42f6e49197fbbe413947eca -r e20408b06d65f4902017bdca1cbc08bc1ec0fdd1 test/tool_shed/functional/test_0420_citable_urls_for_repositories.py --- a/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py +++ b/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py @@ -104,7 +104,6 @@ strings_displayed = [ '/repository/browse_repositories', encoded_user_id, 'operation=repositories_by_user' ] strings_displayed.append( encoded_user_id ) strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420' ] - strings_displayed_in_iframe.append( self.get_repository_tip( repository ) ) self.load_citable_url( username='user1', repository_name=None, changeset_revision=None, @@ -208,7 +207,6 @@ strings_displayed.extend( [ 'list+of+repositories+owned', 'does+not+include+one+named', '%21%21invalid%21%21', 'status=error' ] ) strings_displayed_in_iframe = [ 'user1', 'filtering_0420' ] strings_displayed_in_iframe.append( 'Repositories Owned by user1' ) - strings_displayed_in_iframe.append( tip_revision ) self.load_citable_url( username='user1', repository_name='!!invalid!!', changeset_revision=None, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9854b48f8902/ Changeset: 9854b48f8902 Branch: next-stable User: dan Date: 2014-04-10 22:48:07 Summary: Fix for route used in displaying images on tool installed from a toolshed. Affected #: 1 file diff -r 5b01864ad7902af1174478a9f440cad26927f178 -r 9854b48f89026970f99b004d465ffa63aad54aad lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -284,7 +284,7 @@ # ==================== # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + webapp.add_route( '/admin_toolshed/static/images/:repository_id/{image_file:.+?}', controller='admin_toolshed', action='display_image_in_repository', repository_id=None, https://bitbucket.org/galaxy/galaxy-central/commits/452af6869205/ Changeset: 452af6869205 User: dan Date: 2014-04-10 22:48:31 Summary: merge next-stable Affected #: 1 file diff -r d46493c6d83c13db73209373d2fcaf46e843f4b3 -r 452af6869205b773d42f6e49197fbbe413947eca lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -284,7 +284,7 @@ # ==================== # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + webapp.add_route( '/admin_toolshed/static/images/:repository_id/{image_file:.+?}', controller='admin_toolshed', action='display_image_in_repository', repository_id=None, 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: history API: allow anon users import public datasets into their (only) history, add exception for unknown datatype
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d46493c6d83c/ Changeset: d46493c6d83c User: martenson Date: 2014-04-10 22:45:59 Summary: history API: allow anon users import public datasets into their (only) history, add exception for unknown datatype library API: don't show folders without single accesible item to anonyms Affected #: 5 files diff -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d -r d46493c6d83c13db73209373d2fcaf46e843f4b3 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -60,6 +60,10 @@ status_code = 400 err_code = error_codes.MALFORMED_ID +class UnknownContentsType( MessageException ): + status_code = 400 + err_code = error_codes.UNKNOWN_CONTENTS_TYPE + class RequestParameterMissingException( MessageException ): status_code = 400 err_code = error_codes.USER_REQUEST_MISSING_PARAMETER diff -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d -r d46493c6d83c13db73209373d2fcaf46e843f4b3 lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -50,6 +50,11 @@ "message": "The id of the resource is malformed." }, { + "name": "UNKNOWN_CONTENTS_TYPE", + "code": 400010, + "message": "The request contains unknown type of contents." + }, + { "name": "USER_NO_API_KEY", "code": 403001, "message": "API authentication required for this request" diff -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d -r d46493c6d83c13db73209373d2fcaf46e843f4b3 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -86,40 +86,40 @@ # Return the reversed path so it starts with the library node. full_path = build_path( folder )[::-1] - folder_contents = [] time_updated = '' time_created = '' - # Go through every item in the folder and include its meta-data. + # Go through every accessible item in the folder and include its meta-data. for content_item in self._load_folder_contents( trans, folder ): - return_item = {} - encoded_id = trans.security.encode_id( content_item.id ) - time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) - time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) - - # For folder return also hierarchy values - if content_item.api_type == 'folder': - encoded_id = 'F' + encoded_id - return_item.update ( dict ( item_count = content_item.item_count ) ) + if trans.app.security_agent.can_access_library_item( current_user_roles, content_item, trans.user ): + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) - if content_item.api_type == 'file': - library_dataset_dict = content_item.to_dict() - library_dataset_dict['data_type'] - library_dataset_dict['file_size'] - library_dataset_dict['date_uploaded'] - return_item.update ( dict ( data_type = library_dataset_dict['data_type'], - file_size = library_dataset_dict['file_size'], - date_uploaded = library_dataset_dict['date_uploaded'] ) ) + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id + return_item.update ( dict ( item_count = content_item.item_count ) ) - # For every item return also the default meta-data - return_item.update( dict( id = encoded_id, - type = content_item.api_type, - name = content_item.name, - time_updated = time_updated, - time_created = time_created - ) ) - folder_contents.append( return_item ) + if content_item.api_type == 'file': + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) return { 'metadata' : { 'full_path' : full_path, 'can_add_library_item': can_add_library_item }, 'folder_contents' : folder_contents } diff -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d -r d46493c6d83c13db73209373d2fcaf46e843f4b3 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -190,8 +190,7 @@ hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) return hda_dict - #TODO: allow anon users to copy hdas, ldas - @expose_api + @expose_api_anonymous def create( self, trans, history_id, payload, **kwd ): """ create( self, trans, history_id, payload, **kwd ) @@ -436,10 +435,7 @@ return validated_payload def __handle_unknown_contents_type( self, trans, contents_type ): - # TODO: raise a message exception instead of setting status and returning dict. - trans.response.status = 400 - return { 'error': 'Unknown contents type %s' % type } - + raise exceptions.UnknownContentsType('Unknown contents type: %s' % type) class HDAManager( object ): diff -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d -r d46493c6d83c13db73209373d2fcaf46e843f4b3 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 @@ -12,9 +12,13 @@ import urllib import urllib2 import zipfile -from paste.httpexceptions import HTTPBadRequest -from galaxy import util, web -from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +# from paste.httpexceptions import HTTPBadRequest +from galaxy import util +from galaxy import web +# from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound from galaxy.security import Action from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin @@ -24,7 +28,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): - @web.expose_api + @expose_api_anonymous def show( self, trans, id, **kwd ): """ show( self, trans, id, **kwd ) @@ -41,19 +45,20 @@ try: dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) except Exception, e: - trans.response.status = 500 - return str( e ) - try: - rval = dataset.to_dict() - except Exception, e: - rval = "Error in dataset API at listing contents: " + str( e ) - log.error( rval + ": %s" % str(e), exc_info=True ) - trans.response.status = 500 - return "Error in dataset API at listing contents: " + str( e ) + raise exceptions.ObjectNotFound( 'Requested dataset was not found.' ) + # trans.response.status = 500 + # return str( e ) + # try: + rval = dataset.to_dict() + # except Exception, e: + # rval = "Error in dataset API at listing contents: " + str( e ) + # log.error( rval + ": %s" % str(e), exc_info=True ) + # trans.response.status = 500 + # return "Error in dataset API at listing contents: " + str( e ) rval['id'] = trans.security.encode_id(rval['id']); rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); - rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id']) return rval @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Metrics: initial commit of client side logger
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/12e6db99d151/ Changeset: 12e6db99d151 User: carlfeberhard Date: 2014-04-10 22:28:16 Summary: Metrics: initial commit of client side logger Affected #: 4 files diff -r acec53247232cffb773b2e4a8de67fd3bdc3424e -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var 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g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa 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b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa fa-times").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{new_input_terminal:function(a){var b=$("<div class='terminal input-terminal'></div>")[0];this.enable_input_terminal(b,a.name,a.extensions,a.multiple);return b},enable_input_terminal:function(f,b,d,a){var g=this;var c=f.terminal=new InputTerminal(f,d,a);c.node=g;c.name=b;$(f).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&c.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,c)).redraw()}).bind("hover",function(){if(c.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){$.each(c.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(f).offset().top-2,left:$(f).offset().left-h.width(),"padding-right":$(f).width()}).show()}});g.input_terminals[b]=c},enable_output_terminal:function(d,a,f){var g=this;var c=d;var b=d.terminal=new OutputTerminal(d,f);b.node=g;b.name=a;$(d).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(d.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});g.output_terminals[a]=b},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=d.new_input_terminal(f);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j[0],b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(d){var b=$(this.element),c=this;this.tool_state=d.tool_state;this.form_html=d.form_html;this.tool_errors=d.tool_errors;this.annotation=d.annotation;var f=$.parseJSON(d.post_job_actions);this.post_job_actions=f?f:{};if(this.tool_errors){b.addClass("tool-node-error")}else{b.removeClass("tool-node-error")}var g=b.find("div.inputs");var a=$("<div class='inputs'></div>");$.each(d.data_inputs,function(k,h){var j=c.new_input_terminal(h);g.find("div[name='"+h.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j.terminal.connectors[0]=i;i.handle2=j.terminal}});$(this).remove()});a.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(a);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node(f.type,f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if(!$.isArray(h)){h=[h]}$.each(h,function(k,j){var m=wf.nodes[j.id];var n=new Connector();n.connect(m.output_terminals[j.output_name],d.input_terminals[i]);n.redraw()})}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa fa-times").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}function add_node(b,d,a){var c=prebuild_node(b,d,a);workflow.add_node(c);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview();workflow.activate_node(c);return c}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r acec53247232cffb773b2e4a8de67fd3bdc3424e -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d static/scripts/packed/galaxy.workflows.js --- a/static/scripts/packed/galaxy.workflows.js +++ b/static/scripts/packed/galaxy.workflows.js @@ -1,1 +1,1 @@ -$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal})}else{hide_modal()}show_workflow_parameters()},beforeSubmit:function(h){show_message("Loading workflow","progress")}})}});$(document).ajaxStart(function(){active_ajax_call=true;$(document).bind("ajaxStop.global",function(){active_ajax_call=false})});$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":c,"Auto Re-layout":f,Close:close_editor});function b(){workflow.clear_active_node();$(".right-content").hide();var j="";for(var h in workflow.nodes){var i=workflow.nodes[h];if(i.type=="tool"){j+="<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step "+i.id+" - "+i.name+"</div>";for(var k in i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes to your workflow which will be lost."}};$("div.toolSectionBody").hide();$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var a=null;$("div.toolSectionTitle").each(function(){var g=$(this).next("div.toolSectionBody");$(this).click(function(){if(g.is(":hidden")){if(a){a.slideUp("fast")}a=g;g.slideDown("fast")}else{g.slideUp("fast");a=null}})});async_save_text("workflow-name","workflow-name",rename_async_url,"new_name");$("#workflow-tag").click(function(){$(".tag-area").click();return false});async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,true,4)});function reset(){if(workflow){workflow.remove_all()}workflow=new Workflow($("#canvas-container"))}function scroll_to_nodes(){var a=$("#canvas-viewport");var d=$("#canvas-container");var c,b;if(d.width()<a.width()){b=(a.width()-d.width())/2}else{b=0}if(d.height()<a.height()){c=(a.height()-d.height())/2}else{c=0}d.css({left:b,top:c})}function add_node_for_tool(c,b){var a=prebuild_node("tool",b,c);workflow.add_node(a);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview();workflow.activate_node(a);$.ajax({url:get_new_module_info_url,data:{type:"tool",tool_id:c,_:"true"},global:false,dataType:"json",success:function(d){a.init_field_data(d)},error:function(f,g){var d="error loading field data";if(f.status===0){d+=", server unavailable"}a.error(d)}})}function add_node_for_module(a,b){node=prebuild_node(a,b);workflow.add_node(node);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview();workflow.activate_node(node);$.ajax({url:get_new_module_info_url,data:{type:a,_:"true"},dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status==0){c+=", server unavailable"}node.error(c)}})}function 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f=$("#workflow-parameters-container");var e=$("#workflow-parameters-box");var a="";var d=[];$.each(workflow.nodes,function(g,h){var i=h.form_html.match(c);if(i){d=d.concat(i)}if(h.post_job_actions){$.each(h.post_job_actions,function(j,l){if(l.action_arguments){$.each(l.action_arguments,function(m,n){var o=n.match(c);if(o){d=d.concat(o)}})}});if(d){$.each(d,function(j,l){if($.inArray(l,b)===-1){b.push(l)}})}}});if(b&&b.length!==0){$.each(b,function(g,h){a+="<div>"+h.substring(2,h.length-1)+"</div>"});f.html(a);e.show()}else{f.html(a);e.hide()}}function show_form_for_tool(c,b){$(".right-content").hide();$("#right-content").show().html(c);if(b){$("#right-content").find(".toolForm:first").after("<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Attributes</div><div class='form-row'><label>Annotation / Notes:</label><div style='margin-right: 10px;'><textarea name='annotation' rows='3' style='width: 100%'>"+b.annotation+"</textarea><div class='toolParamHelp'>Add an 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y.consoleLogger.error.apply(y.consoleLogger,z)}else{if(C>=h.WARN&&typeof(y.consoleLogger.warn)==="function"){y.consoleLogger.warn.apply(y.consoleLogger,z)}else{if(C>=h.INFO&&typeof(y.consoleLogger.info)==="function"){y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.DEBUG&&typeof(y.consoleLogger.debug)==="function"){y.consoleLogger.debug.apply(y.consoleLogger,z)}else{if(typeof(y.consoleLogger.log)==="function"){y.consoleLogger.log.apply(y.consoleLogger,z)}}}}}}return y};h.prototype.debug=function l(){this.emit(h.DEBUG,this.options.defaultNamespace,arguments)};h.prototype.log=function g(){this.emit(1,this.options.defaultNamespace,arguments)};h.prototype.info=function u(){this.emit(h.INFO,this.options.defaultNamespace,arguments)};h.prototype.warn=function t(){this.emit(h.WARN,this.options.defaultNamespace,arguments)};h.prototype.error=function p(){this.emit(h.ERROR,this.options.defaultNamespace,arguments)};h.prototype.metric=function n(){this.emit(h.METRIC,this.options.defaultNamespace,arguments)};function w(z){var y=this;y._cache=[];return y._init(z||{})}w.defaultOptions={maxSize:5000};w.prototype._init=function i(y){this.maxSize=y.maxSize||w.defaultOptions.maxSize;return this};w.prototype.add=function k(A){var z=this,y=(z.length()+1)-z.maxSize;if(y>0){z.remove(y)}z._cache.push(z._preprocessEntry(A));return z.length()};w.prototype._preprocessEntry=function q(y){return JSON.stringify(y)};w.prototype.length=function e(){return this._cache.length};w.prototype.get=function v(y){return this._cache.slice(0,y)};w.prototype.remove=function x(y){return this._cache.splice(0,y)};w.prototype.stringify=function o(y){return["[",(this.get(y).join(",\n")),"]"].join("\n")};w.prototype.print=function d(){this._cache.forEach(function(y){console.log(y)})};return{MetricsLogger:h}}); \ No newline at end of file diff -r acec53247232cffb773b2e4a8de67fd3bdc3424e -r 12e6db99d15193b700cbde74f31c71a2ef9bcc2d static/scripts/utils/metrics-logger.js --- /dev/null +++ b/static/scripts/utils/metrics-logger.js @@ -0,0 +1,386 @@ +define([ +], function(){ +/*global window, jQuery, console */ +/*============================================================================= +TODO: + broken pipe due to onunload post in webkit, safari + need to use persistence + +=============================================================================*/ +/** @class MetricsLogger + * + * Object to cache, output, and post log/metric messages to the server. + * Meant to be attached to the Galaxy object. + * + * Log from objects by either attaching logger directly: + * panel.logger.metric( 'user dataset deletion', panel.user.id, hda.toJSON() ) + * or using the LoggableMixin or addLogging function: + * MyBackboneModel.extend( LoggableMixin ).extend({ ... }) + * addLogging( MyBackboneModel, 'my-backbone-model' ) + * + * Log from templates by calling directly from Galaxy object: + * Galaxy.logger.metric( 'template loaded', { ownedByUser : true }); + * + * If you attempt to log an un-serializable object (circular reference, window, etc.), + * that entry will not be cached (or sent). If you set consoleLevel and consoleLogger + * appropriately, a warning will be shown when this happens: + * > panel.metric( 'something weird with window', { window : window }) + * !'Metrics logger could not stringify logArguments: ...' + */ +function MetricsLogger( options ){ + options = options || {}; + var self = this; + + //TODO: this might be used if we store the logs in browser storage + ///** */ + //self.userId = options.userId || null; + + /** the (optional) console to emit logs to */ + self.consoleLogger = options.consoleLogger || null; + + self._init( options ); + return self; +} + +//----------------------------------------------------------------------------- defaults and constants +// see: python std lib, logging +MetricsLogger.ALL = 0; +MetricsLogger.DEBUG = 10; +MetricsLogger.INFO = 20; +MetricsLogger.WARN = 30; +MetricsLogger.ERROR = 40; +// metrics levels here? +//MetricsLogger.MinorEvent = 45; +//MetricsLogger.MajorEvent = 50; +MetricsLogger.METRIC = 50; +MetricsLogger.NONE = 100; + +/** default options - override these through the constructor */ +MetricsLogger.defaultOptions = { + /** if an incoming message has a level >= this, it will be cached - can also be a string (e.g. 'debug') */ + logLevel : MetricsLogger.INFO, + /** if an incoming message has a level >= this, it will be output to the console */ + consoleLevel : MetricsLogger.NONE, + /** the default 'namespace' or label associated with an incoming message (if none is passed) */ + defaultNamespace : 'Galaxy', + /** the prefix attached to client-side logs to distinguish them in the metrics db */ + clientPrefix : 'client.', + + /** the maximum number of messages the cache should hold; if exceeded older messages are removed first */ + maxCacheSize : 3000, + /** the number of messages accumulate before posting to the server; should be <= maxCacheSize */ + postSize : 1000, + /** T/F whether to add a timestamp to incoming cached messages */ + addTime : true, + + /** the relative url to post messages to */ + postUrl : '/api/metrics', + + /** post when the page is unloaded? */// needs to be true if using the LoggingCache (for now) + postOnUnload : true, + + /** an (optional) function that should return an object; used to send additional data with the metrics */ + getPingData : undefined, + /** an (optional) function that will handle the servers response after successfully posting messages */ + onServerResponse : undefined +}; + +//----------------------------------------------------------------------------- set up +/** initialize the logger with options, set up instance vars and cache, and add onpageunload to window */ +MetricsLogger.prototype._init = function _init( options ){ + var self = this; + self.options = {}; + for( var k in MetricsLogger.defaultOptions ){ + if( MetricsLogger.defaultOptions.hasOwnProperty( k ) ){ + self.options[ k ] = ( options.hasOwnProperty( k ) )?( options[ k ] ):( MetricsLogger.defaultOptions[ k ] ); + } + } + self.options.logLevel = self._parseLevel( self.options.logLevel ); + self.options.consoleLevel = self._parseLevel( self.options.consoleLevel ); + //self._emitToConsole( 'debug', 'MetricsLogger', 'MetricsLogger.options:', self.options ); + + self._sending = false; + self._postSize = self.options.postSize; + self._initCache(); + + // post the entire cache on unload (since LoggingCache isn't persistent ATM) + if( self.options.postOnUnload ){ + self.onpageunload = function onpageunload( ev ){ + ev.preventDefault(); + self._postCache({ count: self.cache.length() }); + }; + window.addEventListener( 'unload', self.onpageunload ); + } + + return self; +}; + +/** initialize the cache */ +MetricsLogger.prototype._initCache = function _initCache(){ + this.cache = new LoggingCache({ maxSize : this.options.maxCacheSize }); + +}; + +/** return the numeric log level if level in 'none, debug, log, info, warn, error' */ +MetricsLogger.prototype._parseLevel = function _parseLevel( level ){ + var type = typeof level; + if( type === 'number' ){ return level; } + var upper = level.toUpperCase(); + if( type === 'string' && MetricsLogger.hasOwnProperty( upper ) ){ + return MetricsLogger[ upper ]; + } + throw new Error( 'Unknown log level: ' + level ); +}; + + +//----------------------------------------------------------------------------- main entry point +/** record a log/message's arguments to the cache and/or the console based on level and namespace */ +MetricsLogger.prototype.emit = function emit( level, namespace, logArguments ){ + //this._emitToConsole( 'debug', 'MetricsLogger', [ 'emit:', level, namespace, logArguments ]); + var self = this; + namespace = namespace || self.options.defaultNamespace; + if( !level || !logArguments ){ + return self; + } + // add to cache if proper level +//TODO: respect do not track? + //if( !navigator.doNotTrack && level >= self.options.logLevel ){ + level = self._parseLevel( level ); + if( level >= self.options.logLevel ){ + self._addToCache( level, namespace, logArguments ); + } + // also emit to consoleLogger if proper level for that + if( self.consoleLogger && level >= self.options.consoleLevel ){ + self._emitToConsole( level, namespace, logArguments ); + } + return self; +}; + +//----------------------------------------------------------------------------- cache +/** add a message to the cache and if messages.length is high enough post them to the server */ +MetricsLogger.prototype._addToCache = function _addToCache( level, namespace, logArguments ){ + this._emitToConsole( 'debug', 'MetricsLogger', + [ '_addToCache:', arguments, this.options.addTime, this.cache.length() ]); + //this._emitToConsole( 'debug', 'MetricsLogger', [ '\t logArguments:', logArguments ]); + var self = this; + // try add to the cache and if we've got _postSize number of entries, attempt to post them to the server + try { + var newLength = self.cache.add( self._buildEntry( level, namespace, logArguments ) ); + if( newLength >= self._postSize ){ + self._postCache(); + } + // discard entry if an error occurs, but warn if level set to do so + } catch( err ){ + if( self.options.consoleLevel <= MetricsLogger.WARN ){ + console.warn( 'Metrics logger could not stringify logArguments:', namespace, logArguments ); + console.error( err ); + } + } + return self; +}; + +/** build a log cache entry object from the given level, namespace, and arguments (optionally adding timestamp */ +MetricsLogger.prototype._buildEntry = function _buildEntry( level, namespace, logArguments ){ + this._emitToConsole( 'debug', 'MetricsLogger', [ '_buildEntry:', arguments ]); + var entry = { + level : level, + namespace : this.options.clientPrefix + namespace, + args : logArguments + }; + if( this.options.addTime ){ + entry.time = new Date().toISOString(); + } + return entry; +}; + +/** post _postSize messages from the cache to the server, removing them if successful + * if the post fails, wait until maxCacheSize is accumulated instead and try again then + * in addition to the messages from the cache ('metrics'), any info from getPingData (if set) will be sent + * onServerResponse will be called (if set) with any response from the server + */ +MetricsLogger.prototype._postCache = function _postCache( options ){ + options = options || {}; + this._emitToConsole( 'info', 'MetricsLogger', [ '_postCache', options, this._postSize ]); +//TODO: remove jq dependence + + // short circuit if we're already sending + if( !this.options.postUrl || this._sending ){ + return jQuery.when({}); + } + + var self = this, + postSize = options.count || self._postSize, + // do not splice - remove after *successful* post + entries = self.cache.get( postSize ), + entriesLength = entries.length, + // use the optional getPingData to add any extra info we may want to send + postData = ( typeof self.options.getPingData === 'function' )?( self.options.getPingData() ):( {} ); + //console.debug( postSize, entriesLength ); + + // add the metrics and send + postData.metrics = self._preprocessCache( entries ); + self._sending = true; + return jQuery.post( self.options.postUrl, postData ) + .always( function(){ + self._sending = false; + }) + .fail( function(){ + // if we failed the previous time, set the next post target to the max num of entries + self._postSize = self.options.maxCacheSize; + }) + .done( function( response ){ + if( typeof self.options.onServerResponse === 'function' ){ + self.options.onServerResponse( response ); + } + // only remove if post successful + self.cache.remove( entriesLength ); + console.debug( 'removed entries:', entriesLength, 'size now:', self.cache.length() ); + // if we succeeded, reset the post target to the normal num of entries + self._postSize = self.options.postSize; + }); + // return the xhr promise +}; + +/** Preprocess a number of cache entries for sending to the server (stringification) */ +MetricsLogger.prototype._preprocessCache = function _preprocessCache( entries ){ + return [ '[', ( entries.join( ',\n' ) ), ']' ].join( '\n' ); + //return [ '[', ( entries.join( ',' ) ), ']' ].join( '' ); +}; + + +//----------------------------------------------------------------------------- console +/** output message to console based on level and consoleLogger type */ +MetricsLogger.prototype._emitToConsole = function _emitToConsole( level, namespace, logArguments ){ + //console.debug( '_emitToConsole:', level, namespace, logArguments ); + var self = this; + if( !self.consoleLogger ){ return self; } + + var args = Array.prototype.slice.call( logArguments, 0 ); + args.unshift( namespace ); +//TODO: script location and/or source maps? +//TODO: branch on navigator.userAgent == AIIEEE - it only has log + if( level >= MetricsLogger.METRIC && typeof( self.consoleLogger.info ) === 'function' ){ + return self.consoleLogger.info.apply( self.consoleLogger, args ); + + } else if( level >= MetricsLogger.ERROR && typeof( self.consoleLogger.error ) === 'function' ){ + return self.consoleLogger.error.apply( self.consoleLogger, args ); + } else if( level >= MetricsLogger.WARN && typeof( self.consoleLogger.warn ) === 'function' ){ + self.consoleLogger.warn.apply( self.consoleLogger, args ); + } else if( level >= MetricsLogger.INFO && typeof( self.consoleLogger.info ) === 'function' ){ + self.consoleLogger.info.apply( self.consoleLogger, args ); + } else if( level >= MetricsLogger.DEBUG && typeof( self.consoleLogger.debug ) === 'function' ){ + self.consoleLogger.debug.apply( self.consoleLogger, args ); + } else if( typeof( self.consoleLogger.log ) === 'function' ){ + self.consoleLogger.log.apply( self.consoleLogger, args ); + } + return self; +}; + +//----------------------------------------------------------------------------- shortcuts +// generic functions when logging from non-namespaced object (e.g. templates) +/** debug to default namespace */ +MetricsLogger.prototype.debug = function debug(){ + this.emit( MetricsLogger.DEBUG, this.options.defaultNamespace, arguments ); +}; + +/** log to default namespace */ +MetricsLogger.prototype.log = function log(){ + this.emit( 1, this.options.defaultNamespace, arguments ); +}; + +/** info to default namespace */ +MetricsLogger.prototype.info = function info(){ + this.emit( MetricsLogger.INFO, this.options.defaultNamespace, arguments ); +}; + +/** warn to default namespace */ +MetricsLogger.prototype.warn = function warn(){ + this.emit( MetricsLogger.WARN, this.options.defaultNamespace, arguments ); +}; + +/** error to default namespace */ +MetricsLogger.prototype.error = function error(){ + this.emit( MetricsLogger.ERROR, this.options.defaultNamespace, arguments ); +}; + +/** metric to default namespace */ +MetricsLogger.prototype.metric = function metric(){ + this.emit( MetricsLogger.METRIC, this.options.defaultNamespace, arguments ); +}; + + +//============================================================================= +/** @class LoggingCache + * Simple implementation of cache wrapping an array. + * + * Formats an entry before it's cached and only keeps options.maxSize number + * of entries. Older entries are deleted first. + */ +function LoggingCache( options ){ + var self = this; + self._cache = []; + return self._init( options || {} ); +} + +/** default options */ +LoggingCache.defaultOptions = { + /** maximum number of entries to keep before discarding oldest */ + maxSize : 5000 +}; + +/** initialize with options */ +LoggingCache.prototype._init = function _init( options ){ + this.maxSize = options.maxSize || LoggingCache.defaultOptions.maxSize; + return this; +}; + +/** add an entry to the cache, removing the oldest beforehand if size >= maxSize */ +LoggingCache.prototype.add = function add( entry ){ + var self = this, + overage = ( self.length() + 1 ) - self.maxSize; + if( overage > 0 ){ + self.remove( overage ); + } + self._cache.push( self._preprocessEntry( entry ) ); + return self.length(); +}; + +/** process the entry before caching */ +LoggingCache.prototype._preprocessEntry = function _preprocessEntry( entry ){ + return JSON.stringify( entry ); +}; + +/** return the length --- oh, getters where are you? */ +LoggingCache.prototype.length = function length(){ + return this._cache.length; +}; + +/** get count number of entries starting with the oldest */ +LoggingCache.prototype.get = function get( count ){ + return this._cache.slice( 0, count ); +}; + +/** remove count number of entries starting with the oldest */ +LoggingCache.prototype.remove = function remove( count ){ + return this._cache.splice( 0, count ); +}; + +/** stringify count number of entries (but do not remove) */ +LoggingCache.prototype.stringify = function stringify( count ){ + return [ '[', ( this.get( count ).join( ',\n' ) ), ']' ].join( '\n' ); +}; + +/** outputs entire cache to console */ +LoggingCache.prototype.print = function print(){ + // popup? (really, carl? a popup?) - easier to copy/paste + this._cache.forEach( function( entry ){ + console.log( entry ); + }); +}; + + +//============================================================================= + return { + MetricsLogger : MetricsLogger + }; +}); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Add a link to a tool's toolshed repository if it was installed from a ToolShed.
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/acec53247232/ Changeset: acec53247232 User: dan Date: 2014-04-10 21:55:26 Summary: Add a link to a tool's toolshed repository if it was installed from a ToolShed. Affected #: 1 file diff -r c6d9b2f1b26b219b03a74c321202dc68160e9a15 -r acec53247232cffb773b2e4a8de67fd3bdc3424e templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -378,3 +378,10 @@ </div></div> %endif +%if tool.tool_shed_repository: + <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %> + %if tool_url: + <br/> + ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) } + %endif +%endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: forgotten files for previous commit
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c6d9b2f1b26b/ Changeset: c6d9b2f1b26b User: martenson Date: 2014-04-10 21:07:01 Summary: forgotten files for previous commit data libraries: API refactoring and improvements; backbone decoupling; role UI first implementation Affected #: 4 files diff -r a70f236803f7d398b4f486342e864add77e9ad3f -r c6d9b2f1b26b219b03a74c321202dc68160e9a15 static/scripts/mvc/library/library-folderrow-view.js --- /dev/null +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -0,0 +1,310 @@ +// dependencies +define([ + "galaxy.masthead", + "utils/utils", + "libs/toastr", + "mvc/library/library-model"], +function(mod_masthead, + mod_utils, + mod_toastr, + mod_library_model) { + +// galaxy library row view +var FolderRowView = Backbone.View.extend({ + // last selected history in modal for UX + lastSelectedHistory: '', + + events: { + 'click .library-dataset' : 'showDatasetDetails' + }, + + options: { + type: null + }, + + initialize : function(folder_item){ + this.render(folder_item); + }, + + render: function(folder_item){ + // if (typeof folder_item === 'undefined'){ + // folder_item = Galaxy.libraries.libraryFolderView.collection.get(this.$el.data('id')); + // } + var template = null; + if (folder_item.get('type') === 'folder'){ + this.options.type = 'folder'; + template = this.templateRowFolder(); + } else { + this.options.type = 'file'; + template = this.templateRowFile(); + } + this.setElement(template({content_item:folder_item})); + this.$el.show(); + return this; + }, + + //show modal with current dataset info + showDatasetDetails : function(event){ + // prevent default + event.preventDefault(); + + var id = this.id; + + //create new item + var item = new mod_library_model.Item(); + var histories = new mod_library_model.GalaxyHistories(); + item.id = id; + var self = this; + + //fetch the dataset info + item.fetch({ + success: function (item) { + // TODO can start rendering here already + //fetch user histories for import purposes + histories.fetch({ + success: function (histories){ + self.renderModalAfterFetch(item, histories); + }, + error: function(){ + mod_toastr.error('An error occured during fetching histories:('); + self.renderModalAfterFetch(item); + } + }); + }, + error: function(){ + mod_toastr.error('An error occured during loading dataset details :('); + } + }); +}, + + // show the current dataset in a modal + renderModalAfterFetch : function(item, histories){ + var size = this.size_to_string(item.get('file_size')); + var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + // make modal + var self = this; + this.modal = Galaxy.modal; + this.modal.show({ + closing_events : true, + title : 'Dataset Details', + body : template, + buttons : { + 'Import' : function() { self.importCurrentIntoHistory(); }, + 'Download' : function() { self.downloadCurrent(); }, + 'Close' : function() { self.modal.hide(); } + } + }); + + $(".peek").html(item.get("peek")); + + // show the import-into-history footer only if the request for histories succeeded + if (typeof history.models !== undefined){ + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + } + }, + + // TODO this is dup func, unify + // convert size to nice string + size_to_string : function (size){ + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + + // download dataset shown currently in modal + downloadCurrent : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var library_dataset_id = []; + library_dataset_id.push($('#id_row').attr('data-id')); + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : library_dataset_id}; + + this.processDownload(url, data); + this.modal.enableButton('Import'); + this.modal.enableButton('Download'); + }, + + // TODO this is dup func, unify + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + + mod_toastr.info('Your download will begin soon'); + } + }, + + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use + + var library_dataset_id = $('#id_row').attr('data-id'); + var historyItem = new mod_library_model.HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + + // save the dataset into selected history + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + mod_toastr.success('Dataset imported'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + mod_toastr.error('An error occured! Dataset not imported. Please try again.'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + } + }); + }, + + templateRowFolder: function() { + tmpl_array = []; + + tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder + tmpl_array.push(' <span>(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push('</tr>'); + + return _.template(tmpl_array.join('')); + }, + + templateRowFile: function(){ + tmpl_array = []; + + tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push('</tr>'); + + return _.template(tmpl_array.join('')); + }, + +templateDatasetModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<div class="modal_table">'); + tmpl_array.push(' <table class="grid table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(size) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' </table>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); +}, + +templateHistorySelectInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); +} + +}); + +return { + FolderRowView: FolderRowView +}; + +}); diff -r a70f236803f7d398b4f486342e864add77e9ad3f -r c6d9b2f1b26b219b03a74c321202dc68160e9a15 static/scripts/mvc/library/library-foldertoolbar-view.js --- /dev/null +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -0,0 +1,320 @@ +// dependencies +define([ + "galaxy.masthead", + "utils/utils", + "libs/toastr", + "mvc/library/library-model"], +function(mod_masthead, + mod_utils, + mod_toastr, + mod_library_model) { + +var FolderToolbarView = Backbone.View.extend({ + el: '#center', + + events: { + 'click #toolbtn_create_folder' : 'createFolderFromModal', + 'click #toolbtn_bulk_import' : 'modalBulkImport' + }, + + defaults: { + 'can_add_library_item' : false, + 'contains_file' : false + }, + + modal : null, + + initialize: function(options){ + this.options = _.defaults(options || {}, this.defaults); + this.render(); + }, + + render: function(options){ + this.options = _.extend(this.options, options); + var toolbar_template = this.templateToolBar(); + var is_admin = Galaxy.currUser.isAdmin(); + this.$el.html(toolbar_template({id: this.options.id, admin_user: is_admin})); + }, + + configureElements: function(options){ + this.options = _.extend(this.options, options); + if (this.options.can_add_library_item === true){ + $('#toolbtn_create_folder').show(); + $('#toolbtn_upload_files').show(); + } + if (this.options.contains_file === true){ + $('#toolbtn_bulk_import').show(); + $('#toolbtn_dl').show(); + } + this.$el.find('[data-toggle]').tooltip(); + }, + + // shows modal for creating folder + createFolderFromModal: function(){ + event.preventDefault(); + event.stopPropagation(); + + // create modal + var self = this; + var template = this.templateNewFolderInModal(); + this.modal = Galaxy.modal; + this.modal.show({ + closing_events : true, + title : 'Create New Folder', + body : template(), + buttons : { + 'Create' : function() {self.create_new_folder_event();}, + 'Close' : function() {self.modal.hide(); self.modal = null;} + } + }); + }, + + // create the new folder from modal + create_new_folder_event: function(){ + var folderDetails = this.serialize_new_folder(); + if (this.validate_new_folder(folderDetails)){ + var folder = new mod_library_model.FolderAsModel(); + url_items = Backbone.history.fragment.split('/'); + current_folder_id = url_items[url_items.length-1]; + folder.url = folder.urlRoot + '/' + current_folder_id ; + + var self = this; + folder.save(folderDetails, { + success: function (folder) { + self.modal.hide(); + mod_toastr.success('Folder created'); + Galaxy.libraries.folderListView.render({id: current_folder_id}); + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }); + } else { + mod_toastr.error('Folder\'s name is missing'); + } + return false; + }, + + // serialize data from the modal + serialize_new_folder : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val() + }; + }, + + // validate new folder info + validate_new_folder: function(folderDetails){ + return folderDetails.name !== ''; + }, + + + // show bulk import modal + modalBulkImport : function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length === 0){ + mod_toastr.info('You have to select some datasets first'); + } else { + var self = this; + // fetch histories + var template = this.templateBulkImportInModal(); + var histories = new mod_library_model.GalaxyHistories(); + histories.fetch({ + success: function (histories){ + // make modal + // var history_modal_tmpl = template({histories : histories.models}); + self.modal = Galaxy.modal; + self.modal.show({ + closing_events : true, + title : 'Import into History', + body : template({histories : histories.models}), + buttons : { + 'Import' : function() {self.importAllIntoHistory();}, + 'Close' : function() {self.modal.hide();} + } + }); + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }); + } + }, + + // import all selected datasets into history + importAllIntoHistory : function (){ + //disable the button to prevent multiple submission + this.modal.disableButton('Import'); + + var history_id = $("select[name=dataset_import_bulk] option:selected").val(); + var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id !== '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + var progress_bar_tmpl = this.templateProgressBar(); + $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl({ history_name : history_name })); + + // init the progress bar + var progressStep = 100 / dataset_ids.length; + this.initProgress(progressStep); + + // prepare the dataset objects to be imported + var datasets_to_import = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + library_dataset_id = dataset_ids[i]; + var historyItem = new mod_library_model.HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + historyItem.content = library_dataset_id; + historyItem.source = 'library'; + datasets_to_import.push(historyItem); + } + // call the recursive function to call ajax one after each other (request FIFO queue) + this.chainCall(datasets_to_import); + }, + + chainCall: function(history_item_set){ + var self = this; + var popped_item = history_item_set.pop(); + if (typeof popped_item === "undefined") { + mod_toastr.success('All datasets imported'); + this.modal.hide(); + return; + } + var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ + self.updateProgress(); + self.chainCall(history_item_set); + }); + }, + + initProgress: function(progressStep){ + this.progress = 0; + this.progressStep = progressStep; + }, + + updateProgress: function(){ + this.progress += this.progressStep; + $('.progress-bar-import').width(Math.round(this.progress) + '%'); + txt_representation = Math.round(this.progress) + '% Complete'; + $('.completion_span').text(txt_representation); + }, + + // download selected datasets + download : function(folder_id, format){ + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id !== '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + + var url = '/api/libraries/datasets/download/' + format; + var data = {'ldda_ids' : dataset_ids}; + this.processDownload(url, data, 'get'); + }, + + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + + mod_toastr.info('Your download will begin soon'); + } + }, + + templateToolBar: function(){ + tmpl_array = []; + + // CONTAINER + tmpl_array.push('<div class="library_style_container">'); + tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); + // TOOLBAR + tmpl_array.push('<div id="library_folder_toolbar" >'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload Files to Current Folder" id="toolbtn_upload_files" class="primary-button" type="button" style="display:none;"><span class="fa fa-upload"></span> upload</button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to history</button>'); + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display:none; ">'); + tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' </div>'); + tmpl_array.push(' </div>'); + tmpl_array.push(' <div id="folder_items_element">'); + // library items will append here + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + + templateNewFolderInModal: function(){ + tmpl_array = []; + + tmpl_array.push('<div id="new_folder_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('</form>'); + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + + + templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return _.template(tmpl_array.join('')); + }, + + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return _.template(tmpl_array.join('')); + } +}); + +return { + FolderToolbarView: FolderToolbarView +}; + +}); diff -r a70f236803f7d398b4f486342e864add77e9ad3f -r c6d9b2f1b26b219b03a74c321202dc68160e9a15 static/scripts/packed/mvc/library/library-folderrow-view.js --- /dev/null +++ b/static/scripts/packed/mvc/library/library-folderrow-view.js @@ -0,0 +1,1 @@ +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .library-dataset":"showDatasetDetails"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";g=this.templateRowFile()}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(i){i.preventDefault();var j=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=j;var f=this;h.fetch({success:function(k){g.fetch({success:function(l){f.renderModalAfterFetch(k,l)},error:function(){e.error("An error occured during fetching histories:(");f.renderModalAfterFetch(k)}})},error:function(){e.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new c.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){e.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(){e.error("An error occured! Dataset not imported. Please try again.");g.modal.enableButton("Import");g.modal.enableButton("Download")}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}}); \ No newline at end of file diff -r a70f236803f7d398b4f486342e864add77e9ad3f -r c6d9b2f1b26b219b03a74c321202dc68160e9a15 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- /dev/null +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -0,0 +1,1 @@ +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport"},defaults:{can_add_library_item:false,contains_file:false},modal:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=Galaxy.currUser.isAdmin();this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$("#toolbtn_upload_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){f.modal.hide();f.modal=null}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var h=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;var g=this;h.save(f,{success:function(i){g.modal.hide();e.success("Folder created");Galaxy.libraries.folderListView.render({id:current_folder_id})},error:function(){e.error("An error occured :(")}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var h=this;var i=this.templateBulkImportInModal();var g=new c.GalaxyHistories();g.fetch({success:function(j){h.modal=Galaxy.modal;h.modal.show({closing_events:true,title:"Import into History",body:i({histories:j.models}),buttons:{Import:function(){h.importAllIntoHistory()},Close:function(){h.modal.hide()}}})},error:function(){e.error("An error occured :(")}})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var h=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateProgressBar();$(this.modal.elMain).find(".modal-body").html(n({history_name:m}));var j=100/o.length;this.initProgress(j);var f=[];for(var g=o.length-1;g>=0;g--){library_dataset_id=o[g];var k=new c.HistoryItem();var l=this;k.url=k.urlRoot+h+"/contents";k.content=library_dataset_id;k.source="library";f.push(k)}this.chainCall(f)},chainCall:function(g){var f=this;var h=g.pop();if(typeof h==="undefined"){e.success("All datasets imported");this.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source})).done(function(j){f.updateProgress();f.chainCall(g)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_folder_toolbar" >');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload Files to Current Folder" id="toolbtn_upload_files" class="primary-button" type="button" style="display:none;"><span class="fa fa-upload"></span> upload</button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_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("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: data libraries: API refactoring and improvements; backbone decoupling; role UI first implementation
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a70f236803f7/ Changeset: a70f236803f7 User: martenson Date: 2014-04-10 21:05:33 Summary: data libraries: API refactoring and improvements; backbone decoupling; role UI first implementation Affected #: 19 files diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,13 +1,16 @@ """ -API operations on the contents of a folder. +API operations on the contents of a library folder. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * +from galaxy import util +from galaxy import web +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems +import logging log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @@ -15,65 +18,60 @@ Class controls retrieval, creation and updating of folder contents. """ - def load_folder_contents( self, trans, folder ): - """ - Loads all contents of the folder (folders and data sets) but only in the first level. - """ - current_user_roles = trans.get_current_user_roles() - is_admin = trans.user_is_admin() - content_items = [] - for subfolder in folder.active_folders: - if not is_admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (is_admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - content_items.append( subfolder ) - for dataset in folder.datasets: - if not is_admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) - if (is_admin or can_access) and not dataset.deleted: - dataset.api_type = 'file' - content_items.append( dataset ) - return content_items - - @web.expose_api + @expose_api_anonymous def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. - Full path is provided as a separate object in response providing data for breadcrumb path building. + Full path is provided in response as a separate object providing data for breadcrumb path building. """ - folder_container = [] - current_user_roles = trans.get_current_user_roles() - if ( folder_id.startswith( 'F' ) ): + if ( len( folder_id ) == 17 and folder_id.startswith( 'F' ) ): try: - decoded_folder_id = trans.security.decode_id( folder_id[1:] ) + decoded_folder_id = trans.security.decode_id( folder_id[ 1: ] ) except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) ) + else: + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) ) try: - folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - except: - folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) + folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple folders with same id found.' ) + except NoResultFound: + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + except Exception: + raise exceptions.InternalServerError( 'Error loading from the database.' ) - # We didn't find the folder or user does not have an access to it. - if not folder: - trans.response.status = 400 - return "Invalid folder id ( %s ) specified." % str( folder_id ) - + current_user_roles = trans.get_current_user_roles() + can_add_library_item = trans.user_is_admin() or trans.app.security_agent.can_add_library_item( current_user_roles, folder ) + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): - log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) - trans.response.status = 400 - return "Invalid folder id ( %s ) specified." % str( folder_id ) + if folder.parent_id == None: + try: + library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one() + except Exception: + raise exceptions.InternalServerError( 'Error loading from the database.' ) + if trans.app.security_agent.library_is_public( library, contents=False ): + pass + else: + if trans.user: + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + else: + log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + else: + if trans.user: + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + else: + log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) path_to_root = [] def build_path ( folder ): """ - Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + Search the path upwards recursively and load the whole route of names and ids for breadcrumb building purposes. """ path_to_root = [] # We are almost in root @@ -88,13 +86,13 @@ # Return the reversed path so it starts with the library node. full_path = build_path( folder )[::-1] - folder_container.append( dict( full_path = full_path ) ) + folder_contents = [] time_updated = '' time_created = '' # Go through every item in the folder and include its meta-data. - for content_item in self.load_folder_contents( trans, folder ): + for content_item in self._load_folder_contents( trans, folder ): return_item = {} encoded_id = trans.security.encode_id( content_item.id ) time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) @@ -122,16 +120,36 @@ time_created = time_created ) ) folder_contents.append( return_item ) - # Put the data in the container - folder_container.append( dict( folder_contents = folder_contents ) ) - return folder_container + + return { 'metadata' : { 'full_path' : full_path, 'can_add_library_item': can_add_library_item }, 'folder_contents' : folder_contents } + + def _load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items @web.expose_api def show( self, trans, id, library_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/ """ - pass + raise exceptions.NotImplemented( 'Showing the library folder content is not implemented.' ) @web.expose_api def create( self, trans, library_id, payload, **kwd ): @@ -140,20 +158,21 @@ Creates a new folder. This should be superseded by the LibraryController. """ - pass + raise exceptions.NotImplemented( 'Creating the library folder content is not implemented.' ) @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/folders/{encoded_folder_id}/contents """ - pass + raise exceptions.NotImplemented( 'Updating the library folder content is not implemented.' ) # TODO: Move to library_common. - def __decode_library_content_id( self, trans, content_id ): - if ( len( content_id ) % 16 == 0 ): - return 'LibraryDataset', content_id - elif ( content_id.startswith( 'F' ) ): - return 'LibraryFolder', content_id[1:] - else: - raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) + # def __decode_library_content_id( self, trans, content_id ): + # if ( len( content_id ) % 16 == 0 ): + # return 'LibraryDataset', content_id + # elif ( content_id.startswith( 'F' ) ): + # return 'LibraryFolder', content_id[1:] + # else: + # raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) + diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -1,14 +1,17 @@ """ -API operations on folders +API operations on library folders """ -import logging, os, string, shutil, urllib, re, socket, traceback +import os, string, shutil, urllib, re, socket, traceback from galaxy import datatypes, jobs, web, security +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web.base.controller import BaseAPIController,UsesLibraryMixin,UsesLibraryMixinItems from galaxy.util.sanitize_html import sanitize_html from cgi import escape, FieldStorage from paste.httpexceptions import HTTPBadRequest +import logging log = logging.getLogger( __name__ ) class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @@ -18,9 +21,9 @@ """ GET /api/folders/ This would normally display a list of folders. However, that would - be across multiple libraries, so it's not implemented yet. + be across multiple libraries, so it's not implemented. """ - pass + raise exceptions.NotImplemented( 'Listing all accessible library folders is not implemented.' ) @web.expose_api def show( self, trans, id, **kwd ): diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -7,7 +7,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.model.orm import and_, not_, or_ -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import BaseAPIController import logging log = logging.getLogger( __name__ ) @@ -61,7 +61,6 @@ if trans.app.security_agent.library_is_public( library, contents=False ): item[ 'public' ] = True current_user_roles = trans.get_current_user_roles() - # can_user_add = trans.app.security_agent.can_add_library_item( current_user_roles, library.root_folder ) if not trans.user_is_admin(): item['can_user_add'] = trans.app.security_agent.can_add_library_item( current_user_roles, library ) item['can_user_modify'] = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) @@ -98,7 +97,7 @@ deleted = util.string_as_bool( deleted ) try: decoded_library_id = trans.security.decode_id( library_id ) - except Exception: + except TypeError: raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id ) try: library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) @@ -144,7 +143,14 @@ library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() - return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + + item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + item['can_user_add'] = True + item['can_user_modify'] = True + item['can_user_manage'] = True + if trans.app.security_agent.library_is_public( library, contents=False ): + item[ 'public' ] = True + return item @expose_api def update( self, trans, id, **kwd ): diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -17,8 +17,7 @@ log = logging.getLogger( __name__ ) -class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, - UsesHistoryDatasetAssociationMixin ): +class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ): @expose_api def index( self, trans, library_id, **kwd ): diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -2,28 +2,30 @@ // === MAIN GALAXY LIBRARY MODULE ==== // MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM -// global variables -var library_router = null; - // dependencies define([ - "galaxy.masthead", + "galaxy.masthead", "utils/utils", "libs/toastr", "mvc/base-mvc", "mvc/library/library-model", "mvc/library/library-folderlist-view", "mvc/library/library-librarylist-view", - "mvc/library/library-librarytoolbar-view"], -function(mod_masthead, - mod_utils, + "mvc/library/library-librarytoolbar-view", + "mvc/library/library-foldertoolbar-view" + ], +function(mod_masthead, + mod_utils, mod_toastr, mod_baseMVC, mod_library_model, mod_folderlist_view, mod_librarylist_view, - mod_librarytoolbar_view) { + mod_librarytoolbar_view, + mod_foldertoolbar_view + ) { +// ============================================================================ //ROUTER var LibraryRouter = Backbone.Router.extend({ routes: { @@ -44,12 +46,14 @@ } }); -// galaxy library wrapper View +// ============================================================================ +// Main controller of Galaxy Library var GalaxyLibrary = Backbone.View.extend({ - toolbarView: null, + libraryToolbarView: null, libraryListView: null, library_router: null, - folderContentView: null, + folderToolbarView: null, + folderListView: null, initialize : function(){ Galaxy.libraries = this; @@ -59,25 +63,26 @@ this.library_router.on('route:libraries', function() { // initialize and render the toolbar first - Galaxy.libraries.toolbarView = new mod_librarytoolbar_view.ToolbarView(); + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); // initialize and render libraries second Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); }); this.library_router.on('route:folder_content', function(id) { - // render folder contents - if (!Galaxy.libraries.folderContentView) {Galaxy.libraries.folderContentView = new mod_folderlist_view.FolderContentView();} - Galaxy.libraries.folderContentView.render({id: id}); + // TODO place caching here, sessionstorage/localstorage? + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); }); this.library_router.on('route:download', function(folder_id, format) { - if ($('#center').find(':checked').length === 0) { + if ($('#center').find(':checked').length === 0) { + mod_toastr.info('You have to select some datasets to download') // this happens rarely when there is a server/data error and client gets an actual response instead of an attachment // we don't know what was selected so we can't download again, we redirect to the folder provided Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); } else { // send download stream - Galaxy.libraries.folderContentView.download(folder_id, format); + Galaxy.libraries.folderToolbarView.download(folder_id, format); Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); } }); @@ -86,7 +91,6 @@ } }); -// return return { GalaxyApp: GalaxyLibrary }; diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f 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 @@ -1,458 +1,126 @@ // dependencies define([ - "galaxy.masthead", + "galaxy.masthead", "utils/utils", "libs/toastr", - "mvc/library/library-model"], -function(mod_masthead, - mod_utils, + "mvc/library/library-model", + "mvc/library/library-folderrow-view"], +function(mod_masthead, + mod_utils, mod_toastr, - mod_library_model) { + mod_library_model, + mod_library_folderrow_view) { - //main view for folder browsing -var FolderContentView = Backbone.View.extend({ - // main element definition - el : '#center', - // progress percentage - progress: 0, - // progress rate per one item - progressStep: 1, - // last selected history in modal for UX - lastSelectedHistory: '', - // self modal - modal : null, - // loaded folders - folders : null, +var FolderListView = Backbone.View.extend({ + // main element definition + el : '#folder_items_element', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, + // self modal + modal : null, + folderContainer: null, + + // event binding + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .dataset_row' : 'selectClickedRow' + }, // initialize - initialize : function(){ - this.folders = []; + initialize : function(options){ + var that = this; + this.options = _.defaults(this.options || {}, options); this.queue = jQuery.Deferred(); this.queue.resolve(); - }, -// MMMMMMMMMMMMMMMMMM -// === TEMPLATES ==== -// MMMMMMMMMMMMMMMMMM - - // main template for folder browsing - templateFolder : function (){ - var tmpl_array = []; - - // CONTAINER - tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); - tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); - - // TOOLBAR - tmpl_array.push('<div id="library_folder_toolbar" >'); - tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); - tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>'); - tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); - tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); - tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); - tmpl_array.push(' </button>'); - tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); - tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); - tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); - tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); - tmpl_array.push(' </ul>'); - tmpl_array.push(' </div>'); - - tmpl_array.push('</div>'); - - // BREADCRUMBS - tmpl_array.push('<ol class="breadcrumb">'); - tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); - tmpl_array.push(' <% _.each(path, function(path_item) { %>'); - tmpl_array.push(' <% if (path_item[0] != id) { %>'); - tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); - tmpl_array.push( '<% } else { %>'); - tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</ol>'); - - - // FOLDER CONTENT - tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); - tmpl_array.push(' <thead>'); - tmpl_array.push(' <th class="button_heading"></th>'); - tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th>name</th>'); - tmpl_array.push(' <th>data type</th>'); - tmpl_array.push(' <th>size</th>'); - tmpl_array.push(' <th>date (UTC)</th>'); - tmpl_array.push(' </thead>'); - tmpl_array.push(' <tbody>'); - tmpl_array.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>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% _.each(items, function(content_item) { %>'); - tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder - tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); - tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder - tmpl_array.push(' <span class="muted">(empty folder)</span>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td>folder</td>'); - tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size - tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <tr class="dataset_row light" id="<%- content_item.id %>">'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset - tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type - tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size - tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% } %> '); - tmpl_array.push(' <% }); %>'); - tmpl_array.push(' '); - tmpl_array.push(' </tbody>'); - tmpl_array.push('</table>'); - - tmpl_array.push('</div>'); - return tmpl_array.join(''); - }, - templateDatasetModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<div class="modal_table">'); - tmpl_array.push(' <table class="grid table table-striped table-condensed">'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Data type</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Genome build</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <th scope="row">Size</th>'); - tmpl_array.push(' <td><%= _.escape(size) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Uploaded by</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr scope="row">'); - tmpl_array.push(' <th scope="row">Data Lines</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <th scope="row">Comment Lines</th>'); - tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); - tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <td scope="row">unknown</td>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Number of Columns</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Column Types</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' </table>'); - tmpl_array.push(' <pre class="peek">'); - tmpl_array.push(' </pre>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); - }, - - templateHistorySelectInModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">'); - tmpl_array.push('Select history: '); - tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> '); - tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box - tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</select>'); - tmpl_array.push('</span>'); - - return tmpl_array.join(''); - }, - - templateBulkImportInModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); - tmpl_array.push('Select history: '); - tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); - tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box - tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</select>'); - tmpl_array.push('</span>'); - - return tmpl_array.join(''); - }, - - templateProgressBar : function (){ - var tmpl_array = []; - - tmpl_array.push('<div class="import_text">'); - tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); - tmpl_array.push('</div>'); - tmpl_array.push('<div class="progress">'); - tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); - tmpl_array.push(' <span class="completion_span">0% Complete</span>'); - tmpl_array.push(' </div>'); - tmpl_array.push('</div>'); - tmpl_array.push(''); - - return tmpl_array.join(''); - }, - - templateNewFolderInModal: function(){ - tmpl_array = []; - - tmpl_array.push('<div id="new_folder_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('</form>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); - }, - -// MMMMMMMMMMMMMMM -// === EVENTS ==== -// MMMMMMMMMMMMMMM - - // event binding - events: { - 'click #select-all-checkboxes' : 'selectAll', - 'click #toolbtn_bulk_import' : 'modalBulkImport', - 'click #toolbtn_dl' : 'bulkDownload', - 'click #toolbtn_create_folder' : 'createFolderFromModal', - 'click .library-dataset' : 'showDatasetDetails', - 'click .dataset_row' : 'selectClickedRow' - }, - -// MMMMMMMMMMMMMMMMMM -// === FUNCTIONS ==== -// MMMMMMMMMMMMMMMMMM - - //render the folder view - render: function (options) { - //hack to show scrollbars - $("#center").css('overflow','auto'); - - view = this; - var that = this; - - var folderContainer = new mod_library_model.FolderContainer({id: options.id}); - folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; - - folderContainer.fetch({ - success: function (container) { - - // prepare nice size strings - for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { - var model = folderContainer.attributes.folder.models[i] - if (model.get('type') === 'file'){ - model.set('readable_size', that.size_to_string(model.get('file_size'))) - } - }; - - // find the upper id - var path = folderContainer.full_path; - var upper_folder_id; - if (path.length === 1){ // library is above us - upper_folder_id = 0; - } else { - upper_folder_id = path[path.length-2][0]; - } - - var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); - // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); - that.$el.html(template); - + this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); + this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; + this.folderContainer.fetch({ + success: function (folderContainer) { + that.render(); }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }) - }, - - // convert size to nice string - size_to_string : function (size) - { - // identify unit - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } - // return formatted string - return (Math.round(size) / 10) + unit; - }, - - //show modal with current dataset info - showDatasetDetails : function(event){ - // prevent default - event.preventDefault(); - - //TODO check whether we already have the data - - //load the ID of the row - var id = $(event.target).parent().parent().parent().attr('id'); - if (typeof id === 'undefined'){ - id = $(event.target).parent().attr('id'); - } - if (typeof id === 'undefined'){ - id = $(event.target).parent().parent().attr('id') - } - - //create new item - var item = new mod_library_model.Item(); - var histories = new mod_library_model.GalaxyHistories(); - item.id = id; - var self = this; - - //fetch the dataset info - item.fetch({ - success: function (item) { - // TODO can render here already - //fetch user histories for import purposes - histories.fetch({ - success: function (histories){ - self.renderModalAfterFetch(item, histories) - }, - error: function(){ - mod_toastr.error('An error occured during fetching histories:('); - self.renderModalAfterFetch(item) - } - }); - }, - error: function(){ - mod_toastr.error('An error occured during loading dataset details :('); - } + error: function(){ + mod_toastr.error('An error occured :('); + } }); }, - // show the current dataset in a modal - renderModalAfterFetch : function(item, histories){ - var size = this.size_to_string(item.get('file_size')); - var template = _.template(this.templateDatasetModal(), { item : item, size : size }); - // make modal - var self = this; - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : 'Dataset Details', - body : template, - buttons : { - 'Import' : function() { self.importCurrentIntoHistory() }, - 'Download' : function() { self.downloadCurrent() }, - 'Close' : function() { self.modal.hide() } - } - }); - - $(".peek").html('Peek:' + item.get("peek")); + render: function (options) { + this.options = _.defaults(this.options || {}, options); + var template = this.templateFolder(); + var contains_file = false; - // show the import-into-history footer only if the request for histories succeeded - if (typeof history.models !== undefined){ - var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); - $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); - // preset last selected history if we know it - if (self.lastSelectedHistory.length > 0) { - $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); - } - } - }, + // TODO move to server + // prepare nice size strings + for (var i = 0; i < this.folderContainer.attributes.folder.models.length; i++) { + var model = this.folderContainer.attributes.folder.models[i]; + if (model.get('type') === 'file'){ + contains_file = true; + model.set('readable_size', this.size_to_string(model.get('file_size'))); + } + } - // download dataset shown currently in modal - downloadCurrent : function(){ - //disable the buttons - this.modal.disableButton('Import'); - this.modal.disableButton('Download'); + // TODO move to server + // find the upper id in the full path + var path = this.folderContainer.attributes.metadata.full_path; + var upper_folder_id; + if (path.length === 1){ // the library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } - var library_dataset_id = []; - library_dataset_id.push($('#id_row').attr('data-id')); - var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : library_dataset_id}; + this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, items: this.folderContainer.attributes.folder.models, id: this.options.id, upper_folder_id: upper_folder_id })); - // we assume the view is existent - folderContentView.processDownload(url, data); - this.modal.enableButton('Import'); - this.modal.enableButton('Download'); - }, + if (this.folderContainer.attributes.folder.models.length > 0){ + this.renderRows(); + } + if (this.folderContainer.attributes.metadata.can_add_library_item === true){ + Galaxy.libraries.folderToolbarView.configureElements({ can_add_library_item: this.folderContainer.attributes.metadata.can_add_library_item, contains_file: contains_file }); + } - // import dataset shown currently in modal into selected history - importCurrentIntoHistory : function(){ - //disable the buttons - this.modal.disableButton('Import'); - this.modal.disableButton('Download'); + // initialize the library tooltips + $("#center [data-toggle]").tooltip(); + //hack to show scrollbars + $("#center").css('overflow','auto'); + }, - var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); - this.lastSelectedHistory = history_id; //save selected history for further use + renderRows: function(){ + for (var i = 0; i < this.folderContainer.attributes.folder.models.length; i++) { + var folder_item = this.folderContainer.attributes.folder.models[i]; + var rowView = new mod_library_folderrow_view.FolderRowView(folder_item); + this.$el.find('#folder_list_body').append(rowView.el); + } + }, - var library_dataset_id = $('#id_row').attr('data-id'); - var historyItem = new mod_library_model.HistoryItem(); - var self = this; - historyItem.url = historyItem.urlRoot + history_id + '/contents'; - - // save the dataset into selected history - historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ - mod_toastr.success('Dataset imported'); - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - }, error : function(){ - mod_toastr.error('An error occured! Dataset not imported. Please try again.') - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - } - }); - }, + // convert size to nice string + size_to_string : function (size){ + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, // select all datasets selectAll : function (event) { var selected = event.target.checked; that = this; // Iterate each checkbox - $(':checkbox').each(function () { - this.checked = selected; + $(':checkbox').each(function() { + this.checked = selected; $row = $(this.parentElement.parentElement); // Change color of selected/unselected (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); }); // Show the tools in menu - this.checkTools(); + // this.checkTools(); }, // Check checkbox on row itself or row checkbox click @@ -485,7 +153,7 @@ this.makeWhiteRow($row); } } - this.checkTools(); + // this.checkTools(); }, makeDarkRow: function($row){ @@ -507,207 +175,56 @@ $row.find('span').removeClass('fa-file'); }, - // show toolbar in case something is selected - checkTools : function(){ - var checkedValues = $('#folder_table').find(':checked'); - if(checkedValues.length > 0){ - $('#toolbtn_bulk_import').show(); - $('#toolbtn_dl').show(); - } else { - $('#toolbtn_bulk_import').hide(); - $('#toolbtn_dl').hide(); - } - }, +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM - // show bulk import modal - modalBulkImport : function(){ - var self = this; - // fetch histories - var histories = new mod_library_model.GalaxyHistories(); - histories.fetch({ - success: function (histories){ - // make modal - var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); - self.modal = Galaxy.modal; - self.modal.show({ - closing_events : true, - title : 'Import into History', - body : history_modal_tmpl, - buttons : { - 'Import' : function() {self.importAllIntoHistory()}, - 'Close' : function() {self.modal.hide();} - } - }); - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }); - }, + // main template for folder browsing + templateFolder : function (){ + var tmpl_array = []; - // import all selected datasets into history - importAllIntoHistory : function (){ - //disable the button to prevent multiple submission - this.modal.disableButton('Import'); + // BREADCRUMBS + tmpl_array.push('<ol class="breadcrumb">'); + tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); + tmpl_array.push(' <% _.each(path, function(path_item) { %>'); + tmpl_array.push(' <% if (path_item[0] != id) { %>'); + tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); + tmpl_array.push( '<% } else { %>'); + tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</ol>'); - var history_id = $("select[name=dataset_import_bulk] option:selected").val(); - var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>date (UTC)</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody id="folder_list_body">'); + tmpl_array.push(' <tr>'); + tmpl_array.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>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); - var dataset_ids = []; - $('#folder_table').find(':checked').each(function(){ - if (this.parentElement.parentElement.id != '') { - dataset_ids.push(this.parentElement.parentElement.id); - } - }); - var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); - $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); - // init the progress bar - var progressStep = 100 / dataset_ids.length; - this.initProgress(progressStep); - - // prepare the dataset objects to be imported - var datasets_to_import = []; - for (var i = dataset_ids.length - 1; i >= 0; i--) { - library_dataset_id = dataset_ids[i]; - var historyItem = new mod_library_model.HistoryItem(); - var self = this; - historyItem.url = historyItem.urlRoot + history_id + '/contents'; - historyItem.content = library_dataset_id; - historyItem.source = 'library'; - datasets_to_import.push(historyItem); - }; - - // call the recursive function to call ajax one after each other (request FIFO queue) - this.chainCall(datasets_to_import); - }, - - chainCall: function(history_item_set){ - var self = this; - var popped_item = history_item_set.pop(); - if (typeof popped_item === "undefined") { - mod_toastr.success('All datasets imported'); - this.modal.hide(); - return - } - var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ - self.updateProgress(); - // responses.push(a1); - self.chainCall(history_item_set); - }); - }, - - initProgress: function(progressStep){ - this.progress = 0; - this.progressStep = progressStep; - }, - updateProgress: function(){ - this.progress += this.progressStep; - $('.progress-bar-import').width(Math.round(this.progress) + '%'); - txt_representation = Math.round(this.progress) + '% Complete'; - $('.completion_span').text(txt_representation); - }, - - - - // download selected datasets - download : function(folder_id, format){ - var dataset_ids = []; - $('#folder_table').find(':checked').each(function(){ - if (this.parentElement.parentElement.id != '') { - dataset_ids.push(this.parentElement.parentElement.id); - } - }); - - var url = '/api/libraries/datasets/download/' + format; - var data = {'ldda_ids' : dataset_ids}; - this.processDownload(url, data, 'get'); - }, - - // create hidden form and submit through POST to initialize download - processDownload: function(url, data, method){ - //url and data options required - if( url && data ){ - //data can be string of parameters or array/object - data = typeof data == 'string' ? data : $.param(data); - //split params into form inputs - var inputs = ''; - $.each(data.split('&'), function(){ - var pair = this.split('='); - inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; - }); - //send request - $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') - .appendTo('body').submit().remove(); - - mod_toastr.info('Your download will begin soon'); - }; - }, - - // shows modal for creating folder - createFolderFromModal: function(){ - event.preventDefault(); - event.stopPropagation(); - - // create modal - var self = this; - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : 'Create New Folder', - body : this.templateNewFolderInModal(), - buttons : { - 'Create' : function() {self.create_new_folder_event()}, - 'Close' : function() {self.modal.hide(); self.modal = null;} - } - }); - }, - - // create the new folder from modal - create_new_folder_event: function(){ - var folderDetails = this.serialize_new_folder(); - if (this.validate_new_folder(folderDetails)){ - var folder = new mod_library_model.FolderAsModel(); - - url_items = Backbone.history.fragment.split('/'); - current_folder_id = url_items[url_items.length-1]; - folder.url = folder.urlRoot + '/' + current_folder_id ; - - var self = this; - folder.save(folderDetails, { - success: function (folder) { - self.modal.hide(); - mod_toastr.success('Folder created'); - self.render({id: current_folder_id}); - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }); - } else { - mod_toastr.error('Folder\'s name is missing'); - } - return false; - }, - - // serialize data from the form - serialize_new_folder : function(){ - return { - name: $("input[name='Name']").val(), - description: $("input[name='Description']").val() - }; - }, - - // validate new library info - validate_new_folder: function(folderDetails){ - return folderDetails.name !== ''; + return _.template(tmpl_array.join('')); } }); -// return return { - FolderContentView: FolderContentView + FolderListView: FolderListView }; }); diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/mvc/library/library-librarylist-view.js --- a/static/scripts/mvc/library/library-librarylist-view.js +++ b/static/scripts/mvc/library/library-librarylist-view.js @@ -1,14 +1,14 @@ // dependencies define([ "galaxy.masthead", - "mvc/base-mvc", + "mvc/base-mvc", "utils/utils", "libs/toastr", "mvc/library/library-model", - "mvc/library/library-libraryrow-view"], + "mvc/library/library-libraryrow-view"], function(mod_masthead, - mod_baseMVC, - mod_utils, + mod_baseMVC, + mod_utils, mod_toastr, mod_library_model, mod_library_libraryrow_view) { @@ -29,7 +29,8 @@ rowViews: {}, // initialize - initialize : function(){ + initialize : function(options){ + this.options = _.defaults(this.options || {}, options); var viewContext = this; this.rowViews = {}; @@ -43,7 +44,7 @@ error: function(model, response){ mod_toastr.error('An error occured. Please try again.'); } - }) + }); }, /** Renders the libraries table either from the object's own collection, @@ -52,9 +53,8 @@ render: function (options) { var template = this.templateLibraryList(); var libraries_to_render = null; - var include_deleted = true; var include_deleted = Galaxy.libraries.preferences.get('with_deleted'); - var models = null + var models = null; if (typeof options !== 'undefined'){ include_deleted = typeof options.with_deleted !== 'undefined' ? options.with_deleted : false; models = typeof options.models !== 'undefined' ? options.models : null; @@ -64,7 +64,7 @@ if (include_deleted){ // show all the libraries libraries_to_render = this.collection.models; } else{ // show only undeleted libraries - libraries_to_render = this.collection.where({deleted: false});; + libraries_to_render = this.collection.where({deleted: false}); } } else if (models !== null){ libraries_to_render = models; @@ -74,7 +74,9 @@ this.$el.html(template({length: libraries_to_render.length, order: Galaxy.libraries.preferences.get('sort_order') })); - this.renderRows(libraries_to_render); + if (libraries_to_render.length > 0){ + this.renderRows(libraries_to_render); + } // initialize the library tooltips $("#center [data-toggle]").tooltip(); // modification of upper DOM element to show scrollbars due to the #center element inheritance @@ -92,9 +94,9 @@ var rowView = new mod_library_libraryrow_view.LibraryRowView(library); this.$el.find('#library_list_body').append(rowView.el); // save new rowView to cache - this.rowViews[library.get('id')] = rowView; + this.rowViews[library.get('id')] = rowView; } - }; + } }, sort_clicked : function(){ @@ -115,17 +117,17 @@ if (order === 'asc'){ // this.collection.sort_order = 'asc'; this.collection.comparator = function(libraryA, libraryB){ - if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return 1; // after - if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return -1; // before + if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) {return 1;} // after + if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) {return -1;} // before return 0; // equal - } + }; } else if (order === 'desc'){ // this.collection.sort_order = 'desc'; this.collection.comparator = function(libraryA, libraryB){ - if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return -1; // before - if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return 1; // after + if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) {return -1;} // before + if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) {return 1;} // after return 0; // equal - } + }; } this.collection.sort(); } @@ -140,7 +142,7 @@ tmpl_array.push('<div class="library_container table-responsive">'); tmpl_array.push('<% if(length === 0) { %>'); - tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>"); + tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>'); tmpl_array.push('<% } else{ %>'); tmpl_array.push('<table class="grid table table-condensed">'); tmpl_array.push(' <thead>'); @@ -175,7 +177,7 @@ redirectToHome: function(){ window.location = '../'; - }, + }, redirectToLogin: function(){ window.location = '/user/login'; }, @@ -193,7 +195,7 @@ title : 'Create New Library', body : this.templateNewLibraryInModal(), buttons : { - 'Create' : function() {self.create_new_library_event()}, + 'Create' : function() {self.create_new_library_event();}, 'Close' : function() {self.modal.hide();} } }); @@ -245,7 +247,6 @@ } }); -// return return { LibraryListView: LibraryListView }; diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/mvc/library/library-libraryrow-view.js --- a/static/scripts/mvc/library/library-libraryrow-view.js +++ b/static/scripts/mvc/library/library-libraryrow-view.js @@ -1,11 +1,11 @@ // dependencies define([ - "galaxy.masthead", + "galaxy.masthead", "utils/utils", "libs/toastr", - "mvc/library/library-model"], -function(mod_masthead, - mod_utils, + "mvc/library/library-model"], +function(mod_masthead, + mod_utils, mod_toastr, mod_library_model) { @@ -39,7 +39,7 @@ render: function(library){ if (typeof library === 'undefined'){ - var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data('id')); + library = Galaxy.libraries.libraryListView.collection.get(this.$el.data('id')); } this.prepareButtons(library); var tmpl = this.templateRow(); @@ -51,7 +51,7 @@ repaint: function(library){ /* need to hide manually because of the element removal in setElement invoked in render() */ - $(".tooltip").hide(); + $(".tooltip").hide(); /* we need to store the old element to be able to replace it with new one */ var old_element = this.$el; @@ -83,13 +83,13 @@ vis_config.undelete_library_btn = false; if (library.get('can_user_add') === true){ vis_config.upload_library_btn = true; - } + } if (library.get('can_user_modify') === true){ vis_config.edit_library_btn = true; - } + } if (library.get('can_user_manage') === true){ vis_config.permission_library_btn = true; - } + } } } else if (this.edit_mode === true){ vis_config.upload_library_btn = false; @@ -136,7 +136,7 @@ is_changed = true; } else{ mod_toastr.warning('Library name has to be at least 3 characters long'); - return + return; } } @@ -183,7 +183,7 @@ Galaxy.libraries.libraryListView.collection.add(library); row_view.edit_mode = false; if (Galaxy.libraries.preferences.get('with_deleted') === false){ - $(".tooltip").hide(); + $('.tooltip').hide(); row_view.$el.remove(); } else if (Galaxy.libraries.preferences.get('with_deleted') === true){ row_view.repaint(library); @@ -247,12 +247,11 @@ tmpl_array.push(' </td>'); tmpl_array.push(' </tr>'); - return _.template(tmpl_array.join('')); + return _.template(tmpl_array.join('')); } }); - // return return { LibraryRowView: LibraryRowView }; diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f 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 @@ -1,18 +1,18 @@ // dependencies define([ - "galaxy.masthead", + "galaxy.masthead", "utils/utils", "libs/toastr", - "mvc/library/library-model"], -function(mod_masthead, - mod_utils, + "mvc/library/library-model"], +function(mod_masthead, + mod_utils, mod_toastr, mod_library_model) { -var ToolbarView = Backbone.View.extend({ +var LibraryToolbarView = Backbone.View.extend({ el: '#center', - events: { + events: { 'click #create_new_library_btn' : 'delegate_modal', 'click #include_deleted_chk' : 'check_include_deleted' }, @@ -23,14 +23,16 @@ render: function(){ var toolbar_template = this.templateToolBar(); - this.$el.html(toolbar_template({admin_user: Galaxy.currUser.isAdmin(), anon_user: Galaxy.currUser.isAnonymous()})) + var is_admin = Galaxy.currUser.isAdmin(); + var is_anonym = Galaxy.currUser.isAnonymous(); + this.$el.html(toolbar_template({admin_user: is_admin, anon_user: is_anonym})); if (Galaxy.currUser.isAdmin() === true){ this.$el.find('#include_deleted_chk')[0].checked = Galaxy.libraries.preferences.get('with_deleted'); } }, delegate_modal: function(event){ - // probably should refactor to have this functionality in this view, not in the library view + // probably should refactor to have this functionality in this view, not in the library list view Galaxy.libraries.libraryListView.show_library_modal(event); }, @@ -48,7 +50,7 @@ templateToolBar: function(){ tmpl_array = []; - tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">'); + tmpl_array.push('<div class="library_style_container">'); // TOOLBAR tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">'); tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); @@ -60,16 +62,16 @@ tmpl_array.push(' <% } %>'); tmpl_array.push(' </div>'); tmpl_array.push(' <div id="libraries_element">'); + // table with libraries will append here tmpl_array.push(' </div>'); tmpl_array.push('</div>'); return _.template(tmpl_array.join('')); } -}) +}); -// return return { - ToolbarView: ToolbarView + LibraryToolbarView: LibraryToolbarView }; }); diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -66,16 +66,14 @@ var FolderContainer = Backbone.Model.extend({ defaults : { folder : new Folder(), - full_path : "unknown", urlRoot : "/api/folders/", id : "unknown" }, parse : function(obj) { - this.full_path = obj[0].full_path; - // response is not a simple array, it contains metadata - // this will update the inner collection - this.get("folder").reset(obj[1].folder_contents); - return obj; + // response is not a simple array, it contains metadata + // this will update the inner collection + this.get("folder").reset(obj.folder_contents); + return obj; } }); diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var library_router=null;define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view"],function(e,c,g,j,h,a,f,d){var k=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var i=j.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({toolbarView:null,libraryListView:null,library_router:null,folderContentView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new i({id:"global-lib-prefs"});this.library_router=new k();this.library_router.on("route:libraries",function(){Galaxy.libraries.toolbarView=new d.ToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(l){if(!Galaxy.libraries.folderContentView){Galaxy.libraries.folderContentView=new a.FolderContentView()}Galaxy.libraries.folderContentView.render({id:l})});this.library_router.on("route:download",function(l,m){if($("#center").find(":checked").length===0){Galaxy.libraries.library_router.navigate("folders/"+l,{trigger:true,replace:true})}else{Galaxy.libraries.folderContentView.download(l,m);Galaxy.libraries.library_router.navigate("folders/"+l,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#center").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f 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"],function(a,c,d,b){var e=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var f=[];f.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');f.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');f.push('<div id="library_folder_toolbar" >');f.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');f.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>');f.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');f.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');f.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');f.push(" </button>");f.push(' <ul class="dropdown-menu" role="menu">');f.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');f.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');f.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');f.push(" </ul>");f.push(" </div>");f.push("</div>");f.push('<ol class="breadcrumb">');f.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');f.push(" <% _.each(path, function(path_item) { %>");f.push(" <% if (path_item[0] != id) { %>");f.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');f.push("<% } else { %>");f.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');f.push(" <% } %>");f.push(" <% }); %>");f.push("</ol>");f.push('<table id="folder_table" class="grid table table-condensed">');f.push(" <thead>");f.push(' <th class="button_heading"></th>');f.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');f.push(" <th>name</th>");f.push(" <th>data type</th>");f.push(" <th>size</th>");f.push(" <th>date (UTC)</th>");f.push(" </thead>");f.push(" <tbody>");f.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>');f.push(" <td></td>");f.push(" <td></td>");f.push(" <td></td>");f.push(" <td></td>");f.push(" <td></td>");f.push(" </tr>");f.push(" <% _.each(items, function(content_item) { %>");f.push(' <% if (content_item.get("type") === "folder") { %>');f.push(' <tr class="folder_row light" id="<%- content_item.id %>">');f.push(" <td>");f.push(' <span title="Folder" class="fa fa-folder-o"></span>');f.push(" </td>");f.push(" <td></td>");f.push(" <td>");f.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');f.push(' <% if (content_item.get("item_count") === 0) { %>');f.push(' <span class="muted">(empty folder)</span>');f.push(" <% } %>");f.push(" </td>");f.push(" <td>folder</td>");f.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');f.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');f.push(" </tr>");f.push(" <% } else { %>");f.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');f.push(" <td>");f.push(' <span title="Dataset" class="fa fa-file-o"></span>');f.push(" </td>");f.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');f.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');f.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');f.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');f.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');f.push(" </tr>");f.push(" <% } %> ");f.push(" <% }); %>");f.push(" ");f.push(" </tbody>");f.push("</table>");f.push("</div>");return f.join("")},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")},templateProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return f.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_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("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(f){$("#center").css("overflow","auto");view=this;var h=this;var g=new b.FolderContainer({id:f.id});g.url=g.attributes.urlRoot+f.id+"/contents";g.fetch({success:function(j){for(var l=0;l<g.attributes.folder.models.length;l++){var k=g.attributes.folder.models[l];if(k.get("type")==="file"){k.set("readable_size",h.size_to_string(k.get("file_size")))}}var n=g.full_path;var o;if(n.length===1){o=0}else{o=n[n.length-2][0]}var m=_.template(h.templateFolder(),{path:g.full_path,items:g.attributes.folder.models,id:f.id,upper_folder_id:o});h.$el.html(m)},error:function(){d.error("An error occured :(")}})},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},showDatasetDetails:function(i){i.preventDefault();var j=$(i.target).parent().parent().parent().attr("id");if(typeof j==="undefined"){j=$(i.target).parent().attr("id")}if(typeof j==="undefined"){j=$(i.target).parent().parent().attr("id")}var h=new b.Item();var g=new b.GalaxyHistories();h.id=j;var f=this;h.fetch({success:function(k){g.fetch({success:function(l){f.renderModalAfterFetch(k,l)},error:function(){d.error("An error occured during fetching histories:(");f.renderModalAfterFetch(k)}})},error:function(){d.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html("Peek:"+k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};folderContentView.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new b.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){d.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(){d.error("An error occured! Dataset not imported. Please try again.");g.modal.enableButton("Import");g.modal.enableButton("Download")}})},selectAll:function(g){var f=g.target.checked;that=this;$(":checkbox").each(function(){this.checked=f;$row=$(this.parentElement.parentElement);(f)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(g){var i="";var f;var h;if(g.target.localName==="input"){i=g.target;f=$(g.target.parentElement.parentElement);h="input"}else{if(g.target.localName==="td"){i=$("#"+g.target.parentElement.id).find(":checkbox")[0];f=$(g.target.parentElement);h="td"}}if(i.checked){if(h==="td"){i.checked="";this.makeWhiteRow(f)}else{if(h==="input"){this.makeDarkRow(f)}}}else{if(h==="td"){i.checked="selected";this.makeDarkRow(f)}else{if(h==="input"){this.makeWhiteRow(f)}}}this.checkTools()},makeDarkRow:function(f){f.removeClass("light");f.find("a").removeClass("light");f.addClass("dark");f.find("a").addClass("dark");f.find("span").removeClass("fa-file-o");f.find("span").addClass("fa-file")},makeWhiteRow:function(f){f.removeClass("dark");f.find("a").removeClass("dark");f.addClass("light");f.find("a").addClass("light");f.find("span").addClass("fa-file-o");f.find("span").removeClass("fa-file")},checkTools:function(){var f=$("#folder_table").find(":checked");if(f.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var g=this;var f=new b.GalaxyHistories();f.fetch({success:function(h){var i=_.template(g.templateBulkImportInModal(),{histories:h.models});g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:i,buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){g.modal.hide()}}})},error:function(){d.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var h=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){o.push(this.parentElement.parentElement.id)}});var n=_.template(this.templateProgressBar(),{history_name:m});$(this.modal.elMain).find(".modal-body").html(n);var j=100/o.length;this.initProgress(j);var f=[];for(var g=o.length-1;g>=0;g--){library_dataset_id=o[g];var k=new b.HistoryItem();var l=this;k.url=k.urlRoot+h+"/contents";k.content=library_dataset_id;k.source="library";f.push(k)}this.chainCall(f)},chainCall:function(g){var f=this;var h=g.pop();if(typeof h==="undefined"){d.success("All datasets imported");this.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source})).done(function(j){f.updateProgress();f.chainCall(g)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){f.modal.hide();f.modal=null}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var h=new b.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;var g=this;h.save(f,{success:function(i){g.modal.hide();d.success("Folder created");g.render({id:current_folder_id})},error:function(){d.error("An error occured :(")}})}else{d.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""}});return{FolderContentView:e}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",progress:0,progressStep:1,modal:null,folderContainer:null,events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow"},initialize:function(g){var h=this;this.options=_.defaults(this.options||{},g);this.queue=jQuery.Deferred();this.queue.resolve();this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";this.folderContainer.fetch({success:function(i){h.render()},error:function(){f.error("An error occured :(")}})},render:function(h){this.options=_.defaults(this.options||{},h);var k=this.templateFolder();var l=false;for(var j=0;j<this.folderContainer.attributes.folder.models.length;j++){var g=this.folderContainer.attributes.folder.models[j];if(g.get("type")==="file"){l=true;g.set("readable_size",this.size_to_string(g.get("file_size")))}}var m=this.folderContainer.attributes.metadata.full_path;var n;if(m.length===1){n=0}else{n=m[m.length-2][0]}this.$el.html(k({path:this.folderContainer.attributes.metadata.full_path,items:this.folderContainer.attributes.folder.models,id:this.options.id,upper_folder_id:n}));if(this.folderContainer.attributes.folder.models.length>0){this.renderRows()}if(this.folderContainer.attributes.metadata.can_add_library_item===true){Galaxy.libraries.folderToolbarView.configureElements({can_add_library_item:this.folderContainer.attributes.metadata.can_add_library_item,contains_file:l})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(){for(var j=0;j<this.folderContainer.attributes.folder.models.length;j++){var h=this.folderContainer.attributes.folder.models[j];var g=new a.FolderRowView(h);this.$el.find("#folder_list_body").append(g.el)}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);(g)?that.makeDarkRow($row):that.makeWhiteRow($row)})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(" <th>name</th>");g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>date (UTC)</th>");g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(" <tr>");g.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>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/packed/mvc/library/library-librarylist-view.js --- a/static/scripts/packed/mvc/library/library-librarylist-view.js +++ b/static/scripts/packed/mvc/library/library-librarylist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(){var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(i){h.render()},error:function(j,i){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=true;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));this.renderRows(k);$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(m){for(var l=0;l<m.length;l++){var k=m[l];var j=_.findWhere(this.rowViews,{id:k.get("id")});if(j!==undefined&&this instanceof Backbone.View){j.delegateEvents();this.$el.find("#library_list_body").append(j.el)}else{var h=new a.LibraryRowView(k);this.$el.find("#library_list_body").append(h.el);this.rowViews[k.get("id")]=h}}},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.sortLibraries("name","desc");Galaxy.libraries.preferences.set({sort_order:"desc"})}else{this.sortLibraries("name","asc");Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(i,h){if(i==="name"){if(h==="asc"){this.collection.comparator=function(k,j){if(k.get("name").toLowerCase()>j.get("name").toLowerCase()){return 1}if(j.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}return 0}}else{if(h==="desc"){this.collection.comparator=function(k,j){if(k.get("name").toLowerCase()>j.get("name").toLowerCase()){return -1}if(j.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");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("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(i){i.preventDefault();i.stopPropagation();var h=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){h.create_new_library_event()},Close:function(){h.modal.hide()}}})},create_new_library_event:function(){var j=this.serialize_new_library();if(this.validate_new_library(j)){var i=new c.Library();var h=this;i.save(j,{success:function(k){h.collection.add(k);h.modal.hide();h.clear_library_modal();h.render();e.success("Library created")},error:function(){e.error("An error occured :(")}})}else{e.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(h){return h.name!==""}});return{LibraryListView:f}}); \ No newline at end of file +define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(j){h.render()},error:function(k,j){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(m){for(var l=0;l<m.length;l++){var k=m[l];var j=_.findWhere(this.rowViews,{id:k.get("id")});if(j!==undefined&&this instanceof Backbone.View){j.delegateEvents();this.$el.find("#library_list_body").append(j.el)}else{var h=new a.LibraryRowView(k);this.$el.find("#library_list_body").append(h.el);this.rowViews[k.get("id")]=h}}},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.sortLibraries("name","desc");Galaxy.libraries.preferences.set({sort_order:"desc"})}else{this.sortLibraries("name","asc");Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(i,h){if(i==="name"){if(h==="asc"){this.collection.comparator=function(k,j){if(k.get("name").toLowerCase()>j.get("name").toLowerCase()){return 1}if(j.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}return 0}}else{if(h==="desc"){this.collection.comparator=function(k,j){if(k.get("name").toLowerCase()>j.get("name").toLowerCase()){return -1}if(j.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");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("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(i){i.preventDefault();i.stopPropagation();var h=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){h.create_new_library_event()},Close:function(){h.modal.hide()}}})},create_new_library_event:function(){var j=this.serialize_new_library();if(this.validate_new_library(j)){var i=new c.Library();var h=this;i.save(j,{success:function(k){h.collection.add(k);h.modal.hide();h.clear_library_modal();h.render();e.success("Library created")},error:function(){e.error("An error occured :(")}})}else{e.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(h){return h.name!==""}});return{LibraryListView:f}}); \ No newline at end of file diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/packed/mvc/library/library-libraryrow-view.js --- a/static/scripts/packed/mvc/library/library-libraryrow-view.js +++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .upload_library_btn":"upload_to_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(f){this.render(f)},render:function(g){if(typeof g==="undefined"){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(g);var f=this.templateRow();this.setElement(f({library:g,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(f){$(".tooltip").hide();var g=this.$el;this.render(f);g.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(f){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(f.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(f.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(f.get("can_user_add")===true){vis_config.upload_library_btn=true}if(f.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(f.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true}}this.element_visibility_config=vis_config},upload_to_library:function(){e.info("Coming soon. Stay tuned.")},permissions_on_library:function(){e.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){e.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var h=false;var j=this.$el.find(".input_library_name").val();if(typeof j!=="undefined"&&j!==g.get("name")){if(j.length>2){g.set("name",j);h=true}else{e.warning("Library name has to be at least 3 characters long");return}}var i=this.$el.find(".input_library_description").val();if(typeof i!=="undefined"&&i!==g.get("description")){g.set("description",i);h=true}var k=this.$el.find(".input_library_synopsis").val();if(typeof k!=="undefined"&&k!==g.get("synopsis")){g.set("synopsis",k);h=true}if(h){var f=this;g.save(null,{patch:true,success:function(l){f.edit_mode=false;f.repaint(l);e.success("Changes to library saved")},error:function(m,l){e.error("An error occured during updating the library :(")}})}else{this.edit_mode=false;this.repaint(g);e.info("Nothing has changed")}},delete_library:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var f=this;g.destroy({success:function(h){h.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(h);f.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();f.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){f.repaint(h)}}e.success("Library has been marked deleted")},error:function(){e.error("An error occured during deleting the library :(")}})},undelete_library:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var f=this;g.url=g.urlRoot+g.id+"?undelete=true";g.destroy({success:function(h){h.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(h);f.edit_mode=false;f.repaint(h);e.success("Library has been undeleted")},error:function(){e.error("An error occured while undeleting the library :(")}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if(library.get("deleted") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>');tmpl_array.push(' <% } else if(library.get("public") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button" style="<% if(button_config.upload_library_btn === false) { print("display:none;") } %>"><span class="fa fa-upload"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .upload_library_btn":"upload_to_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(f){this.render(f)},render:function(g){if(typeof g==="undefined"){g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(g);var f=this.templateRow();this.setElement(f({library:g,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(f){$(".tooltip").hide();var g=this.$el;this.render(f);g.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(f){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(f.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(f.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(f.get("can_user_add")===true){vis_config.upload_library_btn=true}if(f.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(f.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true}}this.element_visibility_config=vis_config},upload_to_library:function(){e.info("Coming soon. Stay tuned.")},permissions_on_library:function(){e.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){e.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var h=false;var j=this.$el.find(".input_library_name").val();if(typeof j!=="undefined"&&j!==g.get("name")){if(j.length>2){g.set("name",j);h=true}else{e.warning("Library name has to be at least 3 characters long");return}}var i=this.$el.find(".input_library_description").val();if(typeof i!=="undefined"&&i!==g.get("description")){g.set("description",i);h=true}var k=this.$el.find(".input_library_synopsis").val();if(typeof k!=="undefined"&&k!==g.get("synopsis")){g.set("synopsis",k);h=true}if(h){var f=this;g.save(null,{patch:true,success:function(l){f.edit_mode=false;f.repaint(l);e.success("Changes to library saved")},error:function(m,l){e.error("An error occured during updating the library :(")}})}else{this.edit_mode=false;this.repaint(g);e.info("Nothing has changed")}},delete_library:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var f=this;g.destroy({success:function(h){h.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(h);f.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();f.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){f.repaint(h)}}e.success("Library has been marked deleted")},error:function(){e.error("An error occured during deleting the library :(")}})},undelete_library:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var f=this;g.url=g.urlRoot+g.id+"?undelete=true";g.destroy({success:function(h){h.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(h);f.edit_mode=false;f.repaint(h);e.success("Library has been undeleted")},error:function(){e.error("An error occured while undeleting the library :(")}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if(library.get("deleted") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>');tmpl_array.push(' <% } else if(library.get("public") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button" style="<% if(button_config.upload_library_btn === false) { print("display:none;") } %>"><span class="fa fa-upload"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f 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(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,d,e,c){var b=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();this.$el.html(f({admin_user:Galaxy.currUser.isAdmin(),anon_user:Galaxy.currUser.isAnonymous()}));if(Galaxy.currUser.isAdmin()===true){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(f){Galaxy.libraries.libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.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 id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');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(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});return{ToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,c,d,b){var e=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var h=this.templateToolBar();var g=Galaxy.currUser.isAdmin();var f=Galaxy.currUser.isAnonymous();this.$el.html(h({admin_user:g,anon_user:f}));if(Galaxy.currUser.isAdmin()===true){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(f){Galaxy.libraries.libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.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" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');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(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});return{LibraryToolbarView:e}}); \ No newline at end of file diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/scripts/packed/mvc/library/library-model.js --- a/static/scripts/packed/mvc/library/library-model.js +++ b/static/scripts/packed/mvc/library/library-model.js @@ -1,1 +1,1 @@ -define([],function(){var e=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(k){var j=true;if((!show_delete)&&(this.get("deleted"))){j=false}return j}});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var h=Backbone.Collection.extend({url:"/api/libraries",model:e,sort_key:"name",sort_order:null,initialize:function(j){j=j||{}},getVisible:function(k,l){l=l||[];var j=new h(this.filter(function(m){return m.isVisible(k)}));return j}});var f=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:f});var d=Backbone.Model.extend({defaults:{folder:new c(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(j){this.full_path=j[0].full_path;this.get("folder").reset(j[1].folder_contents);return j}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var g=Backbone.Model.extend({url:"/api/histories/"});var i=Backbone.Collection.extend({url:"/api/histories",model:g});return{Library:e,FolderAsModel:a,Libraries:h,Item:f,Folder:c,FolderContainer:d,HistoryItem:b,GalaxyHistory:g,GalaxyHistories:i}}); \ No newline at end of file +define([],function(){var e=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(k){var j=true;if((!show_delete)&&(this.get("deleted"))){j=false}return j}});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var h=Backbone.Collection.extend({url:"/api/libraries",model:e,sort_key:"name",sort_order:null,initialize:function(j){j=j||{}},getVisible:function(k,l){l=l||[];var j=new h(this.filter(function(m){return m.isVisible(k)}));return j}});var f=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:f});var d=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(j){this.get("folder").reset(j.folder_contents);return j}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var g=Backbone.Model.extend({url:"/api/histories/"});var i=Backbone.Collection.extend({url:"/api/histories",model:g});return{Library:e,FolderAsModel:a,Libraries:h,Item:f,Folder:c,FolderContainer:d,HistoryItem:b,GalaxyHistory:g,GalaxyHistories:i}}); \ No newline at end of file diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1299,6 +1299,7 @@ .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} +.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important} tr.light td{background-color:white;color:black} tr.light:hover td{background-color:#f5e8cc} tr.dark td{background-color:#d6b161;color:white} diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -10,6 +10,7 @@ .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} +.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important} tr.light td{background-color:white;color:black} tr.light:hover td{background-color:#f5e8cc} tr.dark td{background-color:#d6b161;color:white} diff -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c -r a70f236803f7d398b4f486342e864add77e9ad3f static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -49,6 +49,12 @@ } } } +.library_style_container{ + width: 95%; + margin: auto; + margin-top:2em; + overflow: auto !important; +} tr.light td { 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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galaxy-commits April 2014