galaxy-commits June 2013

galaxy-commits@lists.galaxyproject.org

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152 discussions

commit/galaxy-central: guerler: Fix Galaxy CSS utility
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/870ed2858703/ Changeset: 870ed2858703 User: guerler Date: 2013-06-25 20:09:50 Summary: Fix Galaxy CSS utility Affected #: 1 file diff -r 75bc22eefbd917b15d118ebbbe01cb2e01864c0d -r 870ed28587032d80fd955ca31c94bf0977f86165 static/scripts/utils/galaxy.css.js --- a/static/scripts/utils/galaxy.css.js +++ b/static/scripts/utils/galaxy.css.js @@ -28,7 +28,7 @@ function load_file (url) { // check if css is already available - if (!$('link[href="' + url + '"]').length) + if (!$('link[href^="' + url + '"]').length) $('<link href="' + url + '" rel="stylesheet">').appendTo('head'); }; 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: guerler: Update Galaxy Frames CSS
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75bc22eefbd9/ Changeset: 75bc22eefbd9 User: guerler Date: 2013-06-25 16:52:30 Summary: Update Galaxy Frames CSS Affected #: 1 file diff -r f51a4898866a51cfe93c26cf36346a4678a4ca59 -r 75bc22eefbd917b15d118ebbbe01cb2e01864c0d static/style/blue/galaxy.frame.css --- a/static/style/blue/galaxy.frame.css +++ b/static/style/blue/galaxy.frame.css @@ -1,4 +1,7 @@ -body {background: #000000} +/* + galaxy-frames generic styles +*/ + .f-corner { -moz-border-radius: 4px; 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: Dave Bouvier: Fix issue with change_directory action where the target folder would be appended to the full path twice.
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f51a4898866a/ Changeset: f51a4898866a User: Dave Bouvier Date: 2013-06-25 16:44:27 Summary: Fix issue with change_directory action where the target folder would be appended to the full path twice. Affected #: 1 file diff -r e4a8cdf0b3722bbce79a55e5ed7e70306f39885a -r f51a4898866a51cfe93c26cf36346a4678a4ca59 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -313,9 +313,8 @@ extract = action_dict.get( 'extract', False ) common_util.url_download( current_dir, filename, url, extract=extract ) elif action_type == 'change_directory': - target_directory = os.path.realpath( os.path.join( current_dir, dir, action_dict[ 'directory' ] ) ) - current_working_dir = os.path.realpath( dir ) - if target_directory.startswith( current_working_dir ) and os.path.exists( target_directory ): + target_directory = os.path.realpath( os.path.join( current_dir, action_dict[ 'directory' ] ) ) + if target_directory.startswith( os.path.realpath( current_dir ) ) and os.path.exists( target_directory ): dir = target_directory else: log.error( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.', target_directory ) 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: greg: Fix the Galaxy API for installing tool shed repositories when attempting to install a repository that was previously installed but is not longer in the installed state.
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4a8cdf0b372/ Changeset: e4a8cdf0b372 User: greg Date: 2013-06-25 15:51:26 Summary: Fix the Galaxy API for installing tool shed repositories when attempting to install a repository that was previously installed but is not longer in the installed state. Affected #: 1 file diff -r 1cbd7fb4e7e1350a489534779545534d82607db7 -r e4a8cdf0b3722bbce79a55e5ed7e70306f39885a lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -266,11 +266,7 @@ action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) installed_tool_shed_repositories.append( tool_shed_repository_dict ) - elif message: - log.error( message, exc_info=True ) - trans.response.status = 500 - return dict( status='error', error=message ) - elif not created_or_updated_tool_shed_repositories and not message: + else: # We're attempting to install more than 1 repository, and all of them have already been installed. return dict( status='error', error='All repositories that you are attempting to install have been previously installed.' ) # Display the list of installed repositories. 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: greg: Fix recently introduced bug when the download_file action tag implementation was enhanced. This is related to installing tool dependencies along with a tool shed repository.
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1cbd7fb4e7e1/ Changeset: 1cbd7fb4e7e1 User: greg Date: 2013-06-25 14:56:23 Summary: Fix recently introduced bug when the download_file action tag implementation was enhanced. This is related to installing tool dependencies along with a tool shed repository. Affected #: 1 file diff -r 05528b8aa8a1decc291f582b34265918c68f798e -r 1cbd7fb4e7e1350a489534779545534d82607db7 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -194,7 +194,7 @@ # Download a single file to the working directory. filtered_actions = actions[ 1: ] url = action_dict[ 'url' ] - if action_dict[ 'target_filename' ]: + if 'target_filename' in action_dict: # Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this # attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction. filename = action_dict[ 'target_filename' ] 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: greg: Fix for browsing a tool dependency installed with a tol shed repository.
by commits-noreply＠bitbucket.org 25 Jun '13

25 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/05528b8aa8a1/ Changeset: 05528b8aa8a1 User: greg Date: 2013-06-25 12:57:32 Summary: Fix for browsing a tool dependency installed with a tol shed repository. Affected #: 2 files diff -r 80dcf7e41b4aec1d5608c05c870a634651af2924 -r 05528b8aa8a1decc291f582b34265918c68f798e 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 @@ -155,7 +155,8 @@ def browse_tool_dependency( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - tool_dependency = tool_dependency_util.get_tool_dependency( trans, kwd[ 'id' ] ) + tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) if tool_dependency.in_error_state: message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). " message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems " @@ -1166,6 +1167,18 @@ initiate_repository_installation_ids=encoded_repository_ids, reinstalling=True ) + @web.expose + @web.require_admin + def repair_repository( self, trans, **kwd ): + """ + Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as + each repository's tool dependencies. + """ + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_id = kwd[ 'id' ] + tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching diff -r 80dcf7e41b4aec1d5608c05c870a634651af2924 -r 05528b8aa8a1decc291f582b34265918c68f798e templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -863,7 +863,7 @@ ${tool_dependency.name | h} %elif trans.webapp.name == 'galaxy' and tool_dependency.tool_dependency_id: %if tool_dependency.repository_id and tool_dependency.installation_status in [ trans.model.ToolDependency.installation_status.INSTALLED ]: - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.tool_dependency_id ), repository_id=trans.security.encode_id( tool_dependency.repository_id ) )}"> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}"> ${tool_dependency.name | h} </a> %elif tool_dependency.installation_status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Visualizations registry: decompose get_visualzations into both single vis check and all registered check
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/80dcf7e41b4a/ Changeset: 80dcf7e41b4a User: carlfeberhard Date: 2013-06-24 23:47:29 Summary: Visualizations registry: decompose get_visualzations into both single vis check and all registered check Affected #: 1 file diff -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 -r 80dcf7e41b4aec1d5608c05c870a634651af2924 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -98,11 +98,44 @@ """ self.listings = VisualizationsConfigParser.parse( self.configuration_filepath ) - #TODO: def get_visualization( self, trans, visualization_name, target_object ): - # """ - # Is the visualization with the given `visualization_name` applicable - # to the `target_object`? - # """ + def get_visualization( self, trans, visualization_name, target_object ): + """ + Return data to build a url to the visualization with the given + `visualization_name` if it's applicable to `target_object` or + `None` if it's not. + """ + # a little weird to pass trans because this registry is part of the trans.app + listing_data = self.listings.get( visualization_name, None ) + if not listing_data: + return None + + data_sources = listing_data[ 'data_sources' ] + for data_source in data_sources: + # currently a model class is required + model_class = data_source[ 'model_class' ] + if not isinstance( target_object, model_class ): + continue + + # tests are optional - default is the above class test + tests = data_source[ 'tests' ] + if tests and not self.is_object_applicable( trans, target_object, tests ): + continue + + param_data = data_source[ 'to_params' ] + url = self.get_visualization_url( trans, target_object, visualization_name, param_data ) + link_text = listing_data.get( 'link_text', None ) + if not link_text: + # default to visualization name, titlecase, and replace underscores + link_text = visualization_name.title().replace( '_', ' ' ) + render_location = listing_data.get( 'render_location' ) + # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html) + return { + 'href' : url, + 'html' : link_text, + 'target': render_location + } + + return None # -- building links to visualizations from objects -- def get_visualizations( self, trans, target_object ): @@ -111,36 +144,11 @@ the urls to call in order to render the visualizations. """ #TODO:?? a list of objects? YAGNI? - # a little weird to pass trans because this registry is part of the trans.app applicable_visualizations = [] - for vis_name, listing_data in self.listings.items(): - - data_sources = listing_data[ 'data_sources' ] - for data_source in data_sources: - # currently a model class is required - model_class = data_source[ 'model_class' ] - if not isinstance( target_object, model_class ): - continue - - # tests are optional - default is the above class test - tests = data_source[ 'tests' ] - if tests and not self.is_object_applicable( trans, target_object, tests ): - continue - - param_data = data_source[ 'to_params' ] - url = self.get_visualization_url( trans, target_object, vis_name, param_data ) - link_text = listing_data.get( 'link_text', None ) - if not link_text: - # default to visualization name, titlecase, and replace underscores - link_text = vis_name.title().replace( '_', ' ' ) - render_location = listing_data.get( 'render_location' ) - # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html) - applicable_visualizations.append({ - 'href' : url, - 'html' : link_text, - 'target': render_location - }) - + for vis_name in self.listings: + url_data = self.get_visualization( trans, vis_name, target_object ) + if url_data: + applicable_visualizations.append( url_data ) return applicable_visualizations def is_object_applicable( self, trans, target_object, data_source_tests ): 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: greg: Clean up support for installing a tool shed repository that is not in the installed state.
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/208bb69cae38/ Changeset: 208bb69cae38 User: greg Date: 2013-06-24 22:50:05 Summary: Clean up support for installing a tool shed repository that is not in the installed state. Affected #: 4 files diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -216,13 +216,8 @@ tool_path=tool_path, tool_shed_url=tool_shed_url ) # Create the tool_shed_repository database records and gather additional information for repository installation. - created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ repository_util.handle_tool_shed_repositories( trans, installation_dict, using_api=True ) - if message and len( repo_info_dicts ) == 1: - # We're attempting to install a single repository that has already been installed into this Galaxy instance. - log.error( message, exc_info=True ) - trans.response.status = 500 - return dict( status='error', error=message ) if created_or_updated_tool_shed_repositories: # Build the dictionary of information necessary for installing the repositories. installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories, diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 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 @@ -884,15 +884,8 @@ tool_panel_section=tool_panel_section, tool_path=tool_path, tool_shed_url=tool_shed_url ) - created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ repository_util.handle_tool_shed_repositories( trans, installation_dict, using_api=False ) - if message and len( repo_info_dicts ) == 1: - # We're undoubtedly attempting to install a repository that has been previously installed. - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='browse_repositories', - message=message, - status='error' ) ) - if created_or_updated_tool_shed_repositories: installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories, filtered_repo_info_dicts=filtered_repo_info_dicts, @@ -1126,7 +1119,7 @@ repository_dependencies=repository_dependencies ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. - created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ repository_dependency_util.create_repository_dependency_objects( trans=trans, tool_path=tool_path, tool_shed_url=tool_shed_url, diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 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 @@ -358,7 +358,7 @@ tool_panel_section = installation_dict[ 'tool_panel_section' ] tool_path = installation_dict[ 'tool_path' ] tool_shed_url = installation_dict[ 'tool_shed_url' ] - created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ repository_dependency_util.create_repository_dependency_objects( trans=trans, tool_path=tool_path, tool_shed_url=tool_shed_url, @@ -368,11 +368,7 @@ no_changes_checked=no_changes_checked, tool_panel_section=tool_panel_section, new_tool_panel_section=new_tool_panel_section ) - if message and len( repo_info_dicts ) == 1 and not using_api: - installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ] - message += 'Click <a href="%s">here</a> to manage the repository. ' % \ - ( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) ) - return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts def initiate_repository_installation( trans, installation_dict ): # The following installation_dict entries are all required. diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 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 @@ -103,7 +103,6 @@ the dependency relationships between installed repositories. This method is called when new repositories are being installed into a Galaxy instance and when uninstalled repositories are being reinstalled. """ - message = '' # The following list will be maintained within this method to contain all created or updated tool shed repositories, including repository dependencies # that may not be installed. all_created_or_updated_tool_shed_repositories = [] @@ -241,7 +240,7 @@ filtered_repo_info_dicts.append( repo_info_dict ) # Build repository dependency relationships even if the user chose to not install repository dependencies. build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories ) - return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts def generate_message_for_invalid_repository_dependencies( metadata_dict ): """Return the error message associated with an invalid repository dependency for display in the caller.""" 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: Dave Bouvier: Fix bug with installing tool dependencies when new_file_path is not set in the Galaxy configuration file.
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/93e9f520616c/ Changeset: 93e9f520616c User: Dave Bouvier Date: 2013-06-24 22:30:23 Summary: Fix bug with installing tool dependencies when new_file_path is not set in the Galaxy configuration file. Affected #: 1 file diff -r be547fe12a1e1b02bc4c7e79834739c590797526 -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -240,13 +240,13 @@ if istar( file_path ): # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> extract_tar( file_path, install_dir ) - dir = tar_extraction_directory( install_dir, file_path ) + dir = tar_extraction_directory( install_dir, downloaded_file_name ) elif isjar( file_path ): dir = os.path.curdir elif iszip( file_path ): # <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action> zip_archive_extracted = extract_zip( file_path, install_dir ) - dir = zip_extraction_directory( install_dir, file_path ) + dir = zip_extraction_directory( install_dir, downloaded_file_name ) else: dir = install_dir else: 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: greg: Fixes for managing an installed tool shed repository's tool dependencies.
by commits-noreply＠bitbucket.org 24 Jun '13

24 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/be547fe12a1e/ Changeset: be547fe12a1e User: greg Date: 2013-06-24 22:03:59 Summary: Fixes for managing an installed tool shed repository's tool dependencies. Affected #: 5 files diff -r b16265a28cfce30b5678dad9551f08bfdc538ad3 -r be547fe12a1e1b02bc4c7e79834739c590797526 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 @@ -482,9 +482,7 @@ def install_tool_dependencies( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - tool_dependency_ids = util.listify( kwd.get( 'tool_dependency_ids', None ) ) - if not tool_dependency_ids: - tool_dependency_ids = util.listify( kwd.get( 'id', None ) ) + tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) @@ -731,11 +729,11 @@ kwd[ 'status' ] = 'error' installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, tool_shed_repository=tool_shed_repository, - name='tool_dependency_ids', + name='inst_td_ids', uninstalled=False ) uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, tool_shed_repository=tool_shed_repository, - name='tool_dependency_ids', + name='uninstalled_tool_dependency_ids', uninstalled=True ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako', repository=tool_shed_repository, @@ -1517,7 +1515,7 @@ def uninstall_tool_dependencies( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - tool_dependency_ids = util.listify( kwd.get( 'tool_dependency_ids', None ) ) + tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) if not tool_dependency_ids: tool_dependency_ids = util.listify( kwd.get( 'id', None ) ) tool_dependencies = [] diff -r b16265a28cfce30b5678dad9551f08bfdc538ad3 -r be547fe12a1e1b02bc4c7e79834739c590797526 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -220,9 +220,16 @@ def get_tool_dependency_ids( as_string=False, **kwd ): tool_dependency_id = kwd.get( 'tool_dependency_id', None ) - tool_dependency_ids = util.listify( kwd.get( 'tool_dependency_ids', None ) ) - if not tool_dependency_ids: - tool_dependency_ids = util.listify( kwd.get( 'id', None ) ) + if 'tool_dependency_ids' in kwd: + tool_dependency_ids = util.listify( kwd[ 'tool_dependency_ids' ] ) + elif 'id' in kwd: + tool_dependency_ids = util.listify( kwd[ 'id' ] ) + elif 'inst_td_ids' in kwd: + tool_dependency_ids = util.listify( kwd[ 'inst_td_ids' ] ) + elif 'uninstalled_tool_dependency_ids' in kwd: + tool_dependency_ids = util.listify( kwd[ 'uninstalled_tool_dependency_ids' ] ) + else: + tool_dependency_ids = [] if tool_dependency_id and tool_dependency_id not in tool_dependency_ids: tool_dependency_ids.append( tool_dependency_id ) if as_string: diff -r b16265a28cfce30b5678dad9551f08bfdc538ad3 -r be547fe12a1e1b02bc4c7e79834739c590797526 templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -44,7 +44,7 @@ <tr><td> %if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]: - <a target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='browse', id=trans.security.encode_id( tool_dependency.id ) )}"> + <a target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='browse', tool_dependency_ids=trans.security.encode_id( tool_dependency.id ) )}"> ${tool_dependency.name} </a> %else: @@ -66,7 +66,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAll" name="select_all_uninstalled_tool_dependencies_checkbox" value="true" onclick="checkAllFields('tool_dependency_ids');"/><input type="hidden" name="select_all_uninstalled_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b> + <input type="checkbox" id="checkAllUninstalled" name="select_all_uninstalled_tool_dependencies_checkbox" value="true" onclick="checkAllFields( 'uninstalled_tool_dependency_ids', 'checkAllUninstalled' );"/><input type="hidden" name="select_all_uninstalled_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b></div><div style="clear: both"></div><div class="form-row"> @@ -87,7 +87,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <input type="checkbox" id="checkAll" name="select_all_installed_tool_dependencies_checkbox" value="true" onclick="checkAllFields('tool_dependency_ids');"/><input type="hidden" name="select_all_installed_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b> + <input type="checkbox" id="checkAllInstalled" name="select_all_installed_tool_dependencies_checkbox" value="true" onclick="checkAllFields( 'inst_td_ids', 'checkAllInstalled' );"/><input type="hidden" name="select_all_installed_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b></div><div style="clear: both"></div><div class="form-row"> diff -r b16265a28cfce30b5678dad9551f08bfdc538ad3 -r be547fe12a1e1b02bc4c7e79834739c590797526 templates/webapps/tool_shed/common/common.mako --- a/templates/webapps/tool_shed/common/common.mako +++ b/templates/webapps/tool_shed/common/common.mako @@ -1,8 +1,15 @@ -<%def name="common_misc_javascripts()"> +<%def name="common_misc_javascripts( element_id=None )"><script type="text/javascript"> - function checkAllFields( name ) + function checkAllFields( name, element_id=element_id ) { - var chkAll = document.getElementById( 'checkAll' ); + if ( element_id ) + { + chkAll = document.getElementById( element_id ); + } + else + { + var chkAll = document.getElementById( 'checkAll' ); + } var checks = document.getElementsByTagName( 'input' ); var boxLength = checks.length; var allChecked = false; diff -r b16265a28cfce30b5678dad9551f08bfdc538ad3 -r be547fe12a1e1b02bc4c7e79834739c590797526 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -862,12 +862,12 @@ %if row_is_header: ${tool_dependency.name | h} %elif trans.webapp.name == 'galaxy' and tool_dependency.tool_dependency_id: - %if tool_dependency.repository_id and tool_dependency.installation_status == 'Installed': + %if tool_dependency.repository_id and tool_dependency.installation_status in [ trans.model.ToolDependency.installation_status.INSTALLED ]: <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.tool_dependency_id ), repository_id=trans.security.encode_id( tool_dependency.repository_id ) )}"> ${tool_dependency.name | h} </a> - %elif tool_dependency.installation_status != 'Installed': - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', id=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}"> + %elif tool_dependency.installation_status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', tool_dependency_ids=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}"> ${tool_dependency.name} </a> %else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits June 2013