December 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: inithello: Don't try to fetch the nonexistent status element from the dependency tuples.
by commits-noreply＠bitbucket.org 13 Dec '13

13 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45602721c2af/ Changeset: 45602721c2af User: inithello Date: 2013-12-13 17:02:33 Summary: Don't try to fetch the nonexistent status element from the dependency tuples. Affected #: 1 file diff -r 5648e6d15803412cf9467bafd89bfb20d7a5281a -r 45602721c2af7ed02b319110d29fd5e8dcfd20b1 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -89,7 +89,7 @@ <ul> %for installed_dependent_repository_tup in installed_dependent_repositories: <% - tool_shed, name, owner, installed_changeset_revision, status = installed_dependent_repository_tup + tool_shed, name, owner, installed_changeset_revision = installed_dependent_repository_tup %><li>Revision <b>${ installed_changeset_revision | h}</b> of repository <b>${name | h}</b> owned by <b>${owner | h}</b></li> %endfor @@ -100,7 +100,7 @@ <ul> %for td_tup in installed_runtime_dependent_tool_dependencies: <% - tool_shed_repository_id, name, version, type, status = td_tup + tool_shed_repository_id, name, version, type = td_tup containing_repository = irm.get_containing_repository_for_tool_dependency( td_tup ) repository_name = containing_repository.name changeset_revision = containing_repository.changeset_revision 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: jmchilton: casperjs: Fix api-tool-tests.js for recent changes.
by commits-noreply＠bitbucket.org 13 Dec '13

13 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5648e6d15803/ Changeset: 5648e6d15803 User: jmchilton Date: 2013-12-13 16:53:59 Summary: casperjs: Fix api-tool-tests.js for recent changes. Affected #: 2 files diff -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 -r 5648e6d15803412cf9467bafd89bfb20d7a5281a test/casperjs/api-tool-tests.js --- a/test/casperjs/api-tool-tests.js +++ b/test/casperjs/api-tool-tests.js @@ -63,10 +63,10 @@ // =================================================================== TESTS var panelSectionKeys = [ - 'elems', 'id', 'name', 'type', 'version' + 'elems', 'id', 'name', 'version' ], panelToolKeys = [ - 'id', 'name', 'description', 'version', 'link', 'target', 'min_width', 'type' + 'id', 'name', 'description', 'version', 'link', 'target', 'min_width' ], toolSummaryKeys = [ 'id', 'name', 'description', 'version' diff -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 -r 5648e6d15803412cf9467bafd89bfb20d7a5281a test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -331,6 +331,8 @@ this.api.spaceghost.info( 'tools.show: ' + [ id ] ); var data = {}; + data.io_details = true; + return this.api._ajax( utils.format( this.urlTpls.show, id ), { data : data }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Dec '13

13 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d6a9ae1f0dac/ Changeset: d6a9ae1f0dac User: jgoecks Date: 2013-12-13 16:27:00 Summary: Fix location of delete icons for postjob actions in workflows and sample management template. Affected #: 2 files diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r d6a9ae1f0dac526531e937c23d9266c86408454b lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -12,7 +12,7 @@ form = """ if (pja.action_type == "%s"){ p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) @@ -20,7 +20,7 @@ form = """ if (pja.action_type == "%s"){ p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r d6a9ae1f0dac526531e937c23d9266c86408454b templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -314,7 +314,7 @@ %endif %if can_delete_samples: ## Delete button - <td valign="top"><a class="action-button" confirm="This sample is not recoverable after deletion. Click Ok to delete." href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=sample_widget_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> + <td valign="top"><a class="action-button" confirm="This sample is not recoverable after deletion. Click Ok to delete." href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=sample_widget_index )}"><img src="${h.url_for('/static/images/history-buttons/delete_icon.png')}" style="cursor:pointer;"/></a></td> %endif </%def> https://bitbucket.org/galaxy/galaxy-central/commits/9a6419162a6c/ Changeset: 9a6419162a6c User: jgoecks Date: 2013-12-13 16:46:26 Summary: Automated merge. Affected #: 7 files diff -r d6a9ae1f0dac526531e937c23d9266c86408454b -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 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 @@ -66,58 +66,47 @@ # contents (i.e., tool dependencies) require it. if self.status == self.installation_status.UNINSTALLED: return False + this_repository_tup = ( str( self.tool_shed ), + str( self.name ), + str( self.owner ), + str( self.installed_changeset_revision ) ) irm = app.installed_repository_manager # See if this repository's current dependencies are restricted to a single circular relationship. This # means that this repository has a single repository dependency which itself depends upon this repository. - # The repository dependency may have other dependent repositories, but that is not relevant here. - single_repository_dependency = None - for repository in irm.installed_repository_dependencies_of_installed_repositories: - if repository.id == self.id: - installed_repository_dependencies = irm.installed_repository_dependencies_of_installed_repositories[ repository ] - # If this repository defines a circular relationship to another repository, then the list of installed - # repository dependencies will include itself. - if len( installed_repository_dependencies ) == 2: - installed_repository_dependency_ids = [ rd.id for rd in installed_repository_dependencies ] - if self.id in installed_repository_dependency_ids: - # We have a single circular dependency definition, so get the other repository. - for installed_repository_dependency in installed_repository_dependencies: - if installed_repository_dependency != self.id: - single_repository_dependency = installed_repository_dependency - break - if single_repository_dependency is not None: - for repository in irm.installed_repository_dependencies_of_installed_repositories: - if repository.id == single_repository_dependency.id: - installed_repository_dependencies = irm.installed_repository_dependencies_of_installed_repositories[ repository ] - installed_repository_dependency_ids = [ rd.id for rd in installed_repository_dependencies ] - if self.id in installed_repository_dependency_ids: - # This repository is a dependency of the single repository upon which it depends, so we have - # a single circular relationship and this repository can be uninstalled. - return True + # The repository dependency may have other repository dependencies, but that is not relevant here. + single_repository_dependency_tup = None + installed_repository_dependency_tups = \ + irm.installed_repository_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + # If this repository defines a circular relationship to another repository, then the list of tuples + # defining installed repository dependencies will include itself. + if len( installed_repository_dependency_tups ) == 2: + if this_repository_tup in installed_repository_dependency_tups: + # We have a single circular dependency definition, so get the other repository. + for installed_repository_dependency_tup in installed_repository_dependency_tups: + if installed_repository_dependency_tup != this_repository_tup: + single_repository_dependency_tup = installed_repository_dependency_tup + break + if single_repository_dependency_tup is not None: + installed_repository_dependency_tups = \ + irm.installed_repository_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + if this_repository_tup in installed_repository_dependency_tups: + # This repository is a dependency of the single repository upon which it depends, so we have + # a single circular relationship and this repository can be uninstalled. + return True # Find other installed repositories that require this repository. - for repository in irm.installed_dependent_repositories_of_installed_repositories: - if repository.id == self.id: - installed_dependent_repositories = \ - irm.installed_dependent_repositories_of_installed_repositories[ repository ] - if installed_dependent_repositories: - # This repository cannot be uninstalled because other installed repositories require it. - return False + installed_dependent_repositories = \ + irm.installed_dependent_repositories_of_installed_repositories.get( this_repository_tup, [] ) + if installed_dependent_repositories: + # This repository cannot be uninstalled because other installed repositories require it. + return False # Find installed tool dependencies that require this repository's installed tool dependencies. - installed_tool_dependencies = [] - for repository in irm.installed_tool_dependencies_of_installed_repositories: - if repository.id == self.id: - installed_tool_dependencies = \ - irm.installed_tool_dependencies_of_installed_repositories[ repository ] - break - for td in installed_tool_dependencies: - if td.id in irm.ids_of_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies_keys: - for installed_td in irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - if installed_td.id == td.id: - installed_dependent_tds = \ - irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ installed_td ] - if installed_dependent_tds: - # This repository cannot be uninstalled because it contains installed tool dependencies that - # are required at run time by other installed tool dependencies. - return False + installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + for td_tup in installed_tool_dependencies: + installed_dependent_td_tups = irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.get( td_tup, [] ) + if installed_dependent_td_tups: + # This repository cannot be uninstalled because it contains installed tool dependencies that + # are required at run time by other installed tool dependencies. + return False return True @property diff -r d6a9ae1f0dac526531e937c23d9266c86408454b -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -17,13 +17,13 @@ def __init__( self, app ): """ - Among other things, eep in in-memory set of installed repositories and tool dependencies along with the relationships - between each of them. This will allow for quick discovery of those repositories or components that can be uninstalled. - The feature allowing a Galaxy administrator to uninstall a repository should not be available to repositories or tool - dependency packages that are required by other repositories or their contents (packages). The uninstall feature should - be available only at the repository hierarchy level where every dependency will be uninstalled. The exception for this - is if an item (repository or tool dependency package) is not in an INSTALLED state - in these cases, the specific item - can be uninstalled in order to attempt re-installation. + Among other things, keep in in-memory sets of tuples defining installed repositories and tool dependencies along with + the relationships between each of them. This will allow for quick discovery of those repositories or components that + can be uninstalled. The feature allowing a Galaxy administrator to uninstall a repository should not be available to + repositories or tool dependency packages that are required by other repositories or their contents (packages). The + uninstall feature should be available only at the repository hierarchy level where every dependency will be uninstalled. + The exception for this is if an item (repository or tool dependency package) is not in an INSTALLED state - in these + cases, the specific item can be uninstalled in order to attempt re-installation. """ self.app = app self.install_model = self.app.install_model @@ -32,32 +32,35 @@ if self.app.config.migrated_tools_config not in self.tool_configs: self.tool_configs.append( self.app.config.migrated_tools_config ) self.installed_repository_dicts = [] - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of tool_shed_repository objects (whose status can be anything) required by the key. The value defines the - # entire repository dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status can be anything) required by + # the key. The value defines the entire repository dependency tree. self.repository_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of tool_shed_repository objects (whose status is 'Installed') required by the key. The value defines the - # entire repository dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') required by + # the key. The value defines the entire repository dependency tree. self.installed_repository_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of tool_shed_repository objects (whose status is 'Installed') that require the key. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') that require + # the key. self.installed_dependent_repositories_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of its immediate tool_dependency objects (whose status can be anything). The value defines only the immediate - # tool dependencies of the repository and does not include any dependencies of the tool dependencies. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status can be anything). + # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the + # tool dependencies. self.tool_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of its immediate tool_dependency objects (whose status is 'Installed'). The value defines only the immediate - # tool dependencies of the repository and does not include any dependencies of the tool dependencies. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status is 'Installed'). + # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the + # tool dependencies. self.installed_tool_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_dependency objects (whose status is 'Installed') and whose values are - # a list of tool_dependency objects (whose status can be anything) required by the installed tool dependency at runtime. - # The value defines the entire tool dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and + # whose values are a list of tuples defining tool_dependency objects (whose status can be anything) required by the + # installed tool dependency at runtime. The value defines the entire tool dependency tree. self.runtime_tool_dependencies_of_installed_tool_dependencies = {} - # Keep an in-memory dictionary whose keys are tool_dependency objects (whose status is 'Installed') and whose values are - # a list of tool_dependency objects (whose status is 'Installed') that require the key at runtime. The value defines the - # entire tool dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and + # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key + # at runtime. The value defines the entire tool dependency tree. self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} # Load defined dependency relationships for installed tool shed repositories and their contents. self.load_dependency_relationships() @@ -68,101 +71,100 @@ is the population of self.installed_dependent_repositories_of_installed_repositories. Since this method discovers all repositories required by the received repository, it can use the list to add entries to the reverse dictionary. """ + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_shed, name, owner, installed_changeset_revision = repository_tup # Get the list of repository dependencies for this repository. status = self.install_model.ToolShedRepository.installation_status.INSTALLED - repository_dependency_tree = \ - repository_dependency_util.get_repository_dependency_tree_for_repository( self.app, - repository, - status=status ) + repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=status ) # Add an entry to self.installed_repository_dependencies_of_installed_repositories. - if repository.id not in self.ids_of_installed_repository_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + if repository_tup not in self.installed_repository_dependencies_of_installed_repositories: + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to installed_repository_dependencies_of_installed_repositories." log.debug( debug_msg ) - self.installed_repository_dependencies_of_installed_repositories[ repository ] = \ - repository_dependency_tree - # Use the repository_dependency_tree to add entries to the reverse dictionary + self.installed_repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups + # Use the repository_dependency_tups to add entries to the reverse dictionary # self.installed_dependent_repositories_of_installed_repositories. - for required_repository in repository_dependency_tree: - debug_msg = "Appending revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + for required_repository_tup in repository_dependency_tups: + debug_msg = "Appending revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to all dependent repositories in installed_dependent_repositories_of_installed_repositories." log.debug( debug_msg ) - if required_repository.id in self.ids_of_installed_dependent_repositories_of_installed_repositories_keys: - for rd in self.installed_dependent_repositories_of_installed_repositories: - if rd.id == required_repository.id: - self.installed_dependent_repositories_of_installed_repositories[ rd ].append( repository ) - break + if required_repository_tup in self.installed_dependent_repositories_of_installed_repositories: + self.installed_dependent_repositories_of_installed_repositories[ required_repository_tup ].append( repository_tup ) else: - self.installed_dependent_repositories_of_installed_repositories[ required_repository ] = [ repository ] + self.installed_dependent_repositories_of_installed_repositories[ required_repository_tup ] = [ repository_tup ] def add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Add an entry to self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" - if tool_dependency.id not in self.ids_of_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies_keys: - debug_msg = "Adding an entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup not in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Adding an entry for version %s of %s %s " % ( version, type, name ) debug_msg += "to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." log.debug( debug_msg ) status = self.install_model.ToolDependency.installation_status.INSTALLED - installed_runtime_dependent_tool_dependencies = \ - tool_dependency_util.get_runtime_dependent_tool_dependencies( self.app, tool_dependency, status=status ) - self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency ] = \ - installed_runtime_dependent_tool_dependencies + installed_runtime_dependent_tool_dependency_tups = \ + tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=status ) + self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] = \ + installed_runtime_dependent_tool_dependency_tups def add_entry_to_installed_tool_dependencies_of_installed_repositories( self, repository ): """Add an entry to self.installed_tool_dependencies_of_installed_repositories.""" - if repository.id not in self.ids_of_installed_tool_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.installed_tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to installed_tool_dependencies_of_installed_repositories." log.debug( debug_msg ) - installed_tool_dependencies = [] - for td in repository.tool_dependencies: - if td.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: - installed_tool_dependencies.append( td ) - self.installed_tool_dependencies_of_installed_repositories[ repository ] = installed_tool_dependencies + installed_tool_dependency_tups = [] + for tool_dependency in repository.tool_dependencies: + if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + installed_tool_dependency_tups.append( tool_dependency_tup ) + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] = installed_tool_dependency_tups def add_entry_to_repository_dependencies_of_installed_repositories( self, repository ): """Add an entry to self.repository_dependencies_of_installed_repositories.""" - if repository.id not in self.ids_of_repository_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.repository_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to repository_dependencies_of_installed_repositories." log.debug( debug_msg ) - repository_dependency_tree = \ - repository_dependency_util.get_repository_dependency_tree_for_repository( self.app, - repository, - status=None ) - self.repository_dependencies_of_installed_repositories[ repository ] = repository_dependency_tree + repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=None ) + self.repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Add an entry to self.runtime_tool_dependencies_of_installed_tool_dependencies.""" - if tool_dependency.id not in self.ids_of_runtime_tool_dependencies_of_installed_tool_dependencies_keys: - debug_msg = "Adding an entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup not in self.runtime_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Adding an entry for version %s of %s %s " % ( version, type, name ) debug_msg += "to runtime_tool_dependencies_of_installed_tool_dependencies." log.debug( debug_msg ) - runtime_dependent_tool_dependencies = \ - tool_dependency_util.get_runtime_dependent_tool_dependencies( self.app, tool_dependency, status=None ) - self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency ] = \ - runtime_dependent_tool_dependencies + runtime_dependent_tool_dependency_tups = \ + tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=None ) + self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] = \ + runtime_dependent_tool_dependency_tups def add_entry_to_tool_dependencies_of_installed_repositories( self, repository ): """Add an entry to self.tool_dependencies_of_installed_repositories.""" - if repository.id not in self.ids_of_tool_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to tool_dependencies_of_installed_repositories." log.debug( debug_msg ) - self.tool_dependencies_of_installed_repositories[ repository ] = repository.tool_dependencies + tool_dependency_tups = [] + for tool_dependency in repository.tool_dependencies: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + tool_dependency_tups.append( tool_dependency_tup ) + self.tool_dependencies_of_installed_repositories[ repository_tup ] = tool_dependency_tups - def get_containing_repository_for_tool_dependency( self, tool_dependency ): - for installed_repository, tool_dependencies in self.tool_dependencies_of_installed_repositories.items(): - td_ids = [ td.id for td in tool_dependencies ] - if tool_dependency.id in td_ids: - return installed_repository - return None + def get_containing_repository_for_tool_dependency( self, tool_dependency_tup ): + tool_shed_repository_id, name, version, type = tool_dependency_tup + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ).get( tool_shed_repository_id ) def get_repository_install_dir( self, tool_shed_repository ): for tool_config in self.tool_configs: @@ -176,9 +178,9 @@ relative_path = os.path.join( tool_path, ts, 'repos', - tool_shed_repository.owner, - tool_shed_repository.name, - tool_shed_repository.installed_changeset_revision ) + str( tool_shed_repository.owner ), + str( tool_shed_repository.name ), + str( tool_shed_repository.installed_changeset_revision ) ) if os.path.exists( relative_path ): return relative_path return None @@ -202,19 +204,18 @@ def handle_repository_uninstall( self, repository ): """Remove the dependency relationships for a repository that was just uninstalled.""" for tool_dependency in repository.tool_dependencies: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) # Remove this tool_dependency from all values in # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - for td, installed_runtime_dependent_tool_dependencies in \ + for td_tup, installed_runtime_dependent_tool_dependency_tups in \ self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items(): - irdtd_ids = [ irdtd.id for irdtd in installed_runtime_dependent_tool_dependencies ] - if td.id in irdtd_ids: - index = irdtd_ids[ td.id ] + if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups: # Remove the tool_dependency from the list. - del installed_runtime_dependent_tool_dependencies[ index ] + installed_runtime_dependent_tool_dependency_tups.remove( tool_dependency_tup ) # Add the possibly altered list to the altered dictionary. - altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td ] = \ - installed_runtime_dependent_tool_dependencies + altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td_tup ] = \ + installed_runtime_dependent_tool_dependency_tups self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = \ altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies. @@ -239,38 +240,12 @@ # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) # Populate self.installed_tool_dependencies_of_installed_repositories. - for r in self.installed_tool_dependencies_of_installed_repositories: - if r.id == repository.id: - self.installed_tool_dependencies_of_installed_repositories[ r ].append( tool_dependency ) - break - - @property - def ids_of_installed_dependent_repositories_of_installed_repositories_keys( self ): - return [ r.id for r in self.installed_dependent_repositories_of_installed_repositories.keys() ] - - @property - def ids_of_installed_repository_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.installed_repository_dependencies_of_installed_repositories.keys() ] - - @property - def ids_of_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies_keys( self ): - return [ td.id for td in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.keys() ] - - @property - def ids_of_installed_tool_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.installed_tool_dependencies_of_installed_repositories.keys() ] - - @property - def ids_of_repository_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.repository_dependencies_of_installed_repositories.keys() ] - - @property - def ids_of_runtime_tool_dependencies_of_installed_tool_dependencies_keys( self ): - return [ td.id for td in self.runtime_tool_dependencies_of_installed_tool_dependencies.keys() ] - - @property - def ids_of_tool_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.tool_dependencies_of_installed_repositories.keys() ] + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if repository_tup in self.installed_tool_dependencies_of_installed_repositories: + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ].append( tool_dependency_tup ) + else: + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] = [ tool_dependency_tup ] def load_dependency_relationships( self ): """Load relationships for all installed repositories and tool dependencies into in-memnory dictionaries.""" @@ -318,82 +293,76 @@ Remove an entry from self.installed_repository_dependencies_of_installed_repositories. A side-effect of this method is removal of appropriate value items from self.installed_dependent_repositories_of_installed_repositories. """ - # Remove this repository from value lists in self.installed_dependent_repositories_of_installed_repositories. - for r, v in self.installed_dependent_repositories_of_installed_repositories.items(): - rd_ids = [ rd.id for rd in v ] - if repository.id in rd_ids: + # Remove tuples defining this repository from value lists in self.installed_dependent_repositories_of_installed_repositories. + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_shed, name, owner, installed_changeset_revision = repository_tup + altered_installed_dependent_repositories_of_installed_repositories = {} + for r_tup, v_tups in self.installed_dependent_repositories_of_installed_repositories.items(): + if repository_tup in v_tups: debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + ( installed_changeset_revision, name, owner ) + r_tool_shed, r_name, r_owner, r_installed_changeset_revision = r_tup debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % \ - ( str( r.changeset_revision ), str( r.name ), str( r.owner ) ) + ( r_installed_changeset_revision, r_name, r_owner ) debug_msg += "in installed_repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) - new_v = [] - for rd in v: - if rd.id != repository.id: - new_v.append( rd ) - self.installed_dependent_repositories_of_installed_repositories[ r ] = new_v + log.debug( debug_msg ) + v_tups.remove( repository_tup ) + altered_installed_dependent_repositories_of_installed_repositories[ r_tup ] = v_tups + self.installed_dependent_repositories_of_installed_repositories = \ + altered_installed_dependent_repositories_of_installed_repositories # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories. - for r in self.installed_repository_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from installed_repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.installed_repository_dependencies_of_installed_repositories[ r ] - break + if repository_tup in self.installed_repository_dependencies_of_installed_repositories: + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from installed_repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.installed_repository_dependencies_of_installed_repositories[ repository_tup ] def remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Remove an entry from self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" - for td in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - if td.id == tool_dependency.id: - debug_msg = "Removing entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) - debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." - log.debug( debug_msg ) - del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td ] - break + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Removing entry for version %s of %s %s " % ( version, type, name ) + debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." + log.debug( debug_msg ) + del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] def remove_entry_from_installed_tool_dependencies_of_installed_repositories( self, repository ): """Remove an entry from self.installed_tool_dependencies_of_installed_repositories.""" - for r in self.installed_tool_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from installed_tool_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.installed_tool_dependencies_of_installed_repositories[ r ] - break + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.installed_tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from installed_tool_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] def remove_entry_from_repository_dependencies_of_installed_repositories( self, repository ): """Remove an entry from self.repository_dependencies_of_installed_repositories.""" - for r in self.repository_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.repository_dependencies_of_installed_repositories[ r ] - break + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.repository_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.repository_dependencies_of_installed_repositories[ repository_tup ] def remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Remove an entry from self.runtime_tool_dependencies_of_installed_tool_dependencies.""" - for td in self.runtime_tool_dependencies_of_installed_tool_dependencies: - if td.id == tool_dependency.id: - debug_msg = "Removing entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) - debug_msg += "from runtime_tool_dependencies_of_installed_tool_dependencies." - log.debug( debug_msg ) - del self.runtime_tool_dependencies_of_installed_tool_dependencies[ td ] - break + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup in self.runtime_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Removing entry for version %s of %s %s from runtime_tool_dependencies_of_installed_tool_dependencies." % \ + ( version, type, name ) + log.debug( debug_msg ) + del self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] def remove_entry_from_tool_dependencies_of_installed_repositories( self, repository ): """Remove an entry from self.tool_dependencies_of_installed_repositories.""" - for r in self.tool_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from tool_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.tool_dependencies_of_installed_repositories[ r ] - break + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s from tool_dependencies_of_installed_repositories." % \ + ( installed_changeset_revision, name, owner ) + log.debug( debug_msg ) + del self.tool_dependencies_of_installed_repositories[ repository_tup ] diff -r d6a9ae1f0dac526531e937c23d9266c86408454b -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -71,8 +71,8 @@ def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): """ - Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined - by the received repo_info_dict. + Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated + with the repository defined by the received repo_info_dict. """ repository = None installed_rd = {} @@ -102,7 +102,8 @@ # Discover all repository dependencies and retrieve information for installing them. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) - has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) + has_repository_dependencies_only_if_compiling_contained_td = \ + all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) @@ -138,7 +139,8 @@ # We have a single repository with (possibly) no defined repository dependencies. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) - has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) + has_repository_dependencies_only_if_compiling_contained_td = \ + all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) @@ -202,8 +204,8 @@ # Get the description from the metadata in case it has a value. repository_dependencies = metadata.get( 'repository_dependencies', {} ) description = repository_dependencies.get( 'description', None ) - # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the missing_repository_dependencies - # dictionaries for proper display parsing. + # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the + # missing_repository_dependencies dictionaries for proper display parsing. root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, repository.name, repository.owner, diff -r d6a9ae1f0dac526531e937c23d9266c86408454b -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 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 @@ -375,22 +375,32 @@ all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies ) return all_repository_dependencies -def get_repository_dependency_tree_for_repository( app, repository, dependency_tree=None, status=None ): +def get_repository_dependency_tups_for_repository( app, repository, dependency_tups=None, status=None ): """ - Return a list of of tool_shed_repository ids (whose status can be anything) required by the received repository. The - returned list defines the entire repository dependency tree. + Return a list of of tuples defining tool_shed_repository objects (whose status can be anything) required by the + received repository. The returned list defines the entire repository dependency tree. """ - if dependency_tree is None: - dependency_tree = [] - tree_object_ids = [ r.id for r in dependency_tree ] + if dependency_tups is None: + dependency_tups = [] + repository_tup = get_repository_tuple_for_installed_repository_manager( repository ) for rrda in repository.required_repositories: repository_dependency = rrda.repository_dependency required_repository = repository_dependency.repository if status is None or required_repository.status == status: - if required_repository.id not in tree_object_ids: - dependency_tree.append( required_repository ) - return get_repository_dependency_tree_for_repository( app, required_repository, dependency_tree=dependency_tree ) - return dependency_tree + required_repository_tup = get_repository_tuple_for_installed_repository_manager( required_repository ) + if required_repository_tup == repository_tup: + # We have a circular repository dependency relationship, skip this entry. + continue + if required_repository_tup not in dependency_tups: + dependency_tups.append( required_repository_tup ) + return get_repository_dependency_tups_for_repository( app, required_repository, dependency_tups=dependency_tups ) + return dependency_tups + +def get_repository_tuple_for_installed_repository_manager( repository ): + return ( str( repository.tool_shed ), + str( repository.name ), + str( repository.owner ), + str( repository.installed_changeset_revision ) ) def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ): updated_key_rd_dicts = [] @@ -402,9 +412,10 @@ if suc.tool_shed_is_this_tool_shed( rd_toolshed ): repository = suc.get_repository_by_name_and_owner( trans.app, rd_name, rd_owner ) if repository: - repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, - trans.security.encode_id( repository.id ), - rd_changeset_revision ) + repository_metadata = \ + metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + trans.security.encode_id( repository.id ), + rd_changeset_revision ) if repository_metadata: # The repository changeset_revision is installable, so no updates are available. new_key_rd_dict = {} diff -r d6a9ae1f0dac526531e937c23d9266c86408454b -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 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 @@ -200,30 +200,6 @@ tool_dependency_definition_type_class.label return message -def get_runtime_dependent_tool_dependencies( app, tool_dependency, status=None ): - """ - Return the list of tool dependency objects that require the received tool dependency at run time. The returned - list will be filtered by the received status if it is not None. This method is called only from Galaxy. - """ - runtime_dependent_tool_dependencies = [] - required_env_shell_file_path = tool_dependency.get_env_shell_file_path( app ) - if required_env_shell_file_path: - required_env_shell_file_path = os.path.abspath( required_env_shell_file_path ) - if required_env_shell_file_path is not None: - for td in app.install_model.context.query( app.install_model.ToolDependency ): - if status is None or td.status == status: - env_shell_file_path = td.get_env_shell_file_path( app ) - if env_shell_file_path is not None: - try: - contents = open( env_shell_file_path, 'r' ).read() - except Exception, e: - contents = None - log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % \ - ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) - if contents is not None and contents.find( required_env_shell_file_path ) >= 0: - runtime_dependent_tool_dependencies.append( td ) - return runtime_dependent_tool_dependencies - def get_download_url_for_platform( url_templates, platform_info_dict ): ''' Compare the dict returned by get_platform_info() with the values specified in the url_template element. Return @@ -322,6 +298,31 @@ env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) return env_sh_file_path +def get_runtime_dependent_tool_dependency_tuples( app, tool_dependency, status=None ): + """ + Return the list of tool dependency objects that require the received tool dependency at run time. The returned + list will be filtered by the received status if it is not None. This method is called only from Galaxy. + """ + runtime_dependent_tool_dependency_tups = [] + required_env_shell_file_path = tool_dependency.get_env_shell_file_path( app ) + if required_env_shell_file_path: + required_env_shell_file_path = os.path.abspath( required_env_shell_file_path ) + if required_env_shell_file_path is not None: + for td in app.install_model.context.query( app.install_model.ToolDependency ): + if status is None or td.status == status: + env_shell_file_path = td.get_env_shell_file_path( app ) + if env_shell_file_path is not None: + try: + contents = open( env_shell_file_path, 'r' ).read() + except Exception, e: + contents = None + log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % \ + ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) + if contents is not None and contents.find( required_env_shell_file_path ) >= 0: + td_tuple = get_tool_dependency_tuple_for_installed_repository_manager( td ) + runtime_dependent_tool_dependency_tups.append( td_tuple ) + return runtime_dependent_tool_dependency_tups + def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.install_model.context.query( trans.install_model.ToolDependency ).get( trans.security.decode_id( id ) ) @@ -386,6 +387,13 @@ repository_name, repository_changeset_revision ) ) +def get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ): + if tool_dependency.type is None: + type = None + else: + type = str( tool_dependency.type ) + return ( tool_dependency.tool_shed_repository_id, str( tool_dependency.name ), str( tool_dependency.version ), type ) + def handle_tool_dependency_installation_error( app, tool_dependency, error_message, remove_installation_path=False ): # Since there was an installation error, remove the installation directory because the install_package method uses # this: "if os.path.exists( install_dir ):". Setting remove_installation_path to True should rarely occur. It is diff -r d6a9ae1f0dac526531e937c23d9266c86408454b -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -54,32 +54,27 @@ %endif %if not can_uninstall_repository: <% + from tool_shed.util.repository_dependency_util import get_repository_tuple_for_installed_repository_manager + from tool_shed.util.tool_dependency_util import get_tool_dependency_tuple_for_installed_repository_manager + irm = trans.app.installed_repository_manager + repository_tup = get_repository_tuple_for_installed_repository_manager( repository ) # Get installed repositories that this repository requires. installed_dependent_repositories = [] installed_runtime_dependent_tool_dependencies = [] - for r in irm.installed_dependent_repositories_of_installed_repositories: - if r.id == repository.id: - installed_dependent_repositories = irm.installed_dependent_repositories_of_installed_repositories[ r ] - break + installed_dependent_repositories = irm.installed_dependent_repositories_of_installed_repositories.get( repository_tup, [] ) # Get this repository's installed tool dependencies. - installed_tool_dependencies = [] - for r in irm.installed_tool_dependencies_of_installed_repositories: - if r.id == repository.id: - installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories[ r ] - break + installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories.get( repository_tup, [] ) # Get installed runtime dependent tool dependencies of this repository's installed tool dependencies. installed_runtime_dependent_tool_dependencies = [] - for itd in installed_tool_dependencies: - for td in irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - if td.id == itd.id: - installed_dependent_tds = \ - irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td ] - if installed_dependent_tds: - installed_runtime_dependent_tool_dependencies.extend( installed_dependent_tds ) + for itd_tup in installed_tool_dependencies: + installed_dependent_td_tups = \ + irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.get( itd_tup, [] ) + if installed_dependent_td_tups: + installed_runtime_dependent_tool_dependencies.extend( installed_dependent_td_tups ) %> %if installed_dependent_repositories or installed_runtime_dependent_tool_dependencies: <table width="100%" border="0" cellpadding="0" cellspacing="0"> @@ -92,29 +87,28 @@ %if installed_dependent_repositories: <label>Dependent repositories:</label><ul> - %for installed_dependent_repository in installed_dependent_repositories: + %for installed_dependent_repository_tup in installed_dependent_repositories: <% - changeset_revision = installed_dependent_repository.changeset_revision - name = installed_dependent_repository.name - owner = installed_dependent_repository.owner + tool_shed, name, owner, installed_changeset_revision, status = installed_dependent_repository_tup %> - <li>Revision <b>${ changeset_revision | h}</b> of repository <b>${name | h}</b> owned by <b>${owner | h}</b></li> + <li>Revision <b>${ installed_changeset_revision | h}</b> of repository <b>${name | h}</b> owned by <b>${owner | h}</b></li> %endfor </ul> %endif %if installed_runtime_dependent_tool_dependencies: <label>Runtime dependent tool dependencies of this repository's tool dependencies:</label><ul> - %for td in installed_runtime_dependent_tool_dependencies: + %for td_tup in installed_runtime_dependent_tool_dependencies: <% - containing_repository = irm.get_containing_repository_for_tool_dependency( td ) + tool_shed_repository_id, name, version, type, status = td_tup + containing_repository = irm.get_containing_repository_for_tool_dependency( td_tup ) repository_name = containing_repository.name changeset_revision = containing_repository.changeset_revision owner = containing_repository.owner %><li> - Version <b>${td.version}</b> of ${td.type} <b>${td.name}</b> contained in revision - <b>${changeset_revision | h}</b> of repository <b>${repository_name | h}</b> owned by <b>${owner}</b> + Version <b>${version | h}</b> of ${type | h} <b>${name | h}</b> contained in revision + <b>${changeset_revision | h}</b> of repository <b>${repository_name | h}</b> owned by <b>${owner | h}</b></li> %endfor </ul> diff -r d6a9ae1f0dac526531e937c23d9266c86408454b -r 9a6419162a6c31cebdc52ca030b0192c5429bb90 templates/admin/tool_shed_repository/repository_actions_menu.mako --- a/templates/admin/tool_shed_repository/repository_actions_menu.mako +++ b/templates/admin/tool_shed_repository/repository_actions_menu.mako @@ -30,7 +30,6 @@ <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a> - <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ) )}">Repair repository</a> %if repository.can_reset_metadata: <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='reset_repository_metadata', id=trans.security.encode_id( repository.id ) )}">Reset repository metadata</a> %endif @@ -42,6 +41,7 @@ %endif <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a> %endif + <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ) )}">Repair repository</a></div></ul></%def> 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: Use tuples to define objects in Galaxy's installed_repository_manager.
by commits-noreply＠bitbucket.org 13 Dec '13

13 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f2731f3baec8/ Changeset: f2731f3baec8 User: greg Date: 2013-12-13 16:35:49 Summary: Use tuples to define objects in Galaxy's installed_repository_manager. Affected #: 7 files diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r f2731f3baec83e5ebf038ac703164b3f4ee53a72 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 @@ -66,58 +66,47 @@ # contents (i.e., tool dependencies) require it. if self.status == self.installation_status.UNINSTALLED: return False + this_repository_tup = ( str( self.tool_shed ), + str( self.name ), + str( self.owner ), + str( self.installed_changeset_revision ) ) irm = app.installed_repository_manager # See if this repository's current dependencies are restricted to a single circular relationship. This # means that this repository has a single repository dependency which itself depends upon this repository. - # The repository dependency may have other dependent repositories, but that is not relevant here. - single_repository_dependency = None - for repository in irm.installed_repository_dependencies_of_installed_repositories: - if repository.id == self.id: - installed_repository_dependencies = irm.installed_repository_dependencies_of_installed_repositories[ repository ] - # If this repository defines a circular relationship to another repository, then the list of installed - # repository dependencies will include itself. - if len( installed_repository_dependencies ) == 2: - installed_repository_dependency_ids = [ rd.id for rd in installed_repository_dependencies ] - if self.id in installed_repository_dependency_ids: - # We have a single circular dependency definition, so get the other repository. - for installed_repository_dependency in installed_repository_dependencies: - if installed_repository_dependency != self.id: - single_repository_dependency = installed_repository_dependency - break - if single_repository_dependency is not None: - for repository in irm.installed_repository_dependencies_of_installed_repositories: - if repository.id == single_repository_dependency.id: - installed_repository_dependencies = irm.installed_repository_dependencies_of_installed_repositories[ repository ] - installed_repository_dependency_ids = [ rd.id for rd in installed_repository_dependencies ] - if self.id in installed_repository_dependency_ids: - # This repository is a dependency of the single repository upon which it depends, so we have - # a single circular relationship and this repository can be uninstalled. - return True + # The repository dependency may have other repository dependencies, but that is not relevant here. + single_repository_dependency_tup = None + installed_repository_dependency_tups = \ + irm.installed_repository_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + # If this repository defines a circular relationship to another repository, then the list of tuples + # defining installed repository dependencies will include itself. + if len( installed_repository_dependency_tups ) == 2: + if this_repository_tup in installed_repository_dependency_tups: + # We have a single circular dependency definition, so get the other repository. + for installed_repository_dependency_tup in installed_repository_dependency_tups: + if installed_repository_dependency_tup != this_repository_tup: + single_repository_dependency_tup = installed_repository_dependency_tup + break + if single_repository_dependency_tup is not None: + installed_repository_dependency_tups = \ + irm.installed_repository_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + if this_repository_tup in installed_repository_dependency_tups: + # This repository is a dependency of the single repository upon which it depends, so we have + # a single circular relationship and this repository can be uninstalled. + return True # Find other installed repositories that require this repository. - for repository in irm.installed_dependent_repositories_of_installed_repositories: - if repository.id == self.id: - installed_dependent_repositories = \ - irm.installed_dependent_repositories_of_installed_repositories[ repository ] - if installed_dependent_repositories: - # This repository cannot be uninstalled because other installed repositories require it. - return False + installed_dependent_repositories = \ + irm.installed_dependent_repositories_of_installed_repositories.get( this_repository_tup, [] ) + if installed_dependent_repositories: + # This repository cannot be uninstalled because other installed repositories require it. + return False # Find installed tool dependencies that require this repository's installed tool dependencies. - installed_tool_dependencies = [] - for repository in irm.installed_tool_dependencies_of_installed_repositories: - if repository.id == self.id: - installed_tool_dependencies = \ - irm.installed_tool_dependencies_of_installed_repositories[ repository ] - break - for td in installed_tool_dependencies: - if td.id in irm.ids_of_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies_keys: - for installed_td in irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - if installed_td.id == td.id: - installed_dependent_tds = \ - irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ installed_td ] - if installed_dependent_tds: - # This repository cannot be uninstalled because it contains installed tool dependencies that - # are required at run time by other installed tool dependencies. - return False + installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + for td_tup in installed_tool_dependencies: + installed_dependent_td_tups = irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.get( td_tup, [] ) + if installed_dependent_td_tups: + # This repository cannot be uninstalled because it contains installed tool dependencies that + # are required at run time by other installed tool dependencies. + return False return True @property diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r f2731f3baec83e5ebf038ac703164b3f4ee53a72 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -17,13 +17,13 @@ def __init__( self, app ): """ - Among other things, eep in in-memory set of installed repositories and tool dependencies along with the relationships - between each of them. This will allow for quick discovery of those repositories or components that can be uninstalled. - The feature allowing a Galaxy administrator to uninstall a repository should not be available to repositories or tool - dependency packages that are required by other repositories or their contents (packages). The uninstall feature should - be available only at the repository hierarchy level where every dependency will be uninstalled. The exception for this - is if an item (repository or tool dependency package) is not in an INSTALLED state - in these cases, the specific item - can be uninstalled in order to attempt re-installation. + Among other things, keep in in-memory sets of tuples defining installed repositories and tool dependencies along with + the relationships between each of them. This will allow for quick discovery of those repositories or components that + can be uninstalled. The feature allowing a Galaxy administrator to uninstall a repository should not be available to + repositories or tool dependency packages that are required by other repositories or their contents (packages). The + uninstall feature should be available only at the repository hierarchy level where every dependency will be uninstalled. + The exception for this is if an item (repository or tool dependency package) is not in an INSTALLED state - in these + cases, the specific item can be uninstalled in order to attempt re-installation. """ self.app = app self.install_model = self.app.install_model @@ -32,32 +32,35 @@ if self.app.config.migrated_tools_config not in self.tool_configs: self.tool_configs.append( self.app.config.migrated_tools_config ) self.installed_repository_dicts = [] - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of tool_shed_repository objects (whose status can be anything) required by the key. The value defines the - # entire repository dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status can be anything) required by + # the key. The value defines the entire repository dependency tree. self.repository_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of tool_shed_repository objects (whose status is 'Installed') required by the key. The value defines the - # entire repository dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') required by + # the key. The value defines the entire repository dependency tree. self.installed_repository_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of tool_shed_repository objects (whose status is 'Installed') that require the key. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') that require + # the key. self.installed_dependent_repositories_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of its immediate tool_dependency objects (whose status can be anything). The value defines only the immediate - # tool dependencies of the repository and does not include any dependencies of the tool dependencies. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status can be anything). + # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the + # tool dependencies. self.tool_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_shed_repository objects (whose status is 'Installed') and whose values - # are a list of its immediate tool_dependency objects (whose status is 'Installed'). The value defines only the immediate - # tool dependencies of the repository and does not include any dependencies of the tool dependencies. + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status is 'Installed'). + # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the + # tool dependencies. self.installed_tool_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tool_dependency objects (whose status is 'Installed') and whose values are - # a list of tool_dependency objects (whose status can be anything) required by the installed tool dependency at runtime. - # The value defines the entire tool dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and + # whose values are a list of tuples defining tool_dependency objects (whose status can be anything) required by the + # installed tool dependency at runtime. The value defines the entire tool dependency tree. self.runtime_tool_dependencies_of_installed_tool_dependencies = {} - # Keep an in-memory dictionary whose keys are tool_dependency objects (whose status is 'Installed') and whose values are - # a list of tool_dependency objects (whose status is 'Installed') that require the key at runtime. The value defines the - # entire tool dependency tree. + # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and + # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key + # at runtime. The value defines the entire tool dependency tree. self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} # Load defined dependency relationships for installed tool shed repositories and their contents. self.load_dependency_relationships() @@ -68,101 +71,100 @@ is the population of self.installed_dependent_repositories_of_installed_repositories. Since this method discovers all repositories required by the received repository, it can use the list to add entries to the reverse dictionary. """ + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_shed, name, owner, installed_changeset_revision = repository_tup # Get the list of repository dependencies for this repository. status = self.install_model.ToolShedRepository.installation_status.INSTALLED - repository_dependency_tree = \ - repository_dependency_util.get_repository_dependency_tree_for_repository( self.app, - repository, - status=status ) + repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=status ) # Add an entry to self.installed_repository_dependencies_of_installed_repositories. - if repository.id not in self.ids_of_installed_repository_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + if repository_tup not in self.installed_repository_dependencies_of_installed_repositories: + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to installed_repository_dependencies_of_installed_repositories." log.debug( debug_msg ) - self.installed_repository_dependencies_of_installed_repositories[ repository ] = \ - repository_dependency_tree - # Use the repository_dependency_tree to add entries to the reverse dictionary + self.installed_repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups + # Use the repository_dependency_tups to add entries to the reverse dictionary # self.installed_dependent_repositories_of_installed_repositories. - for required_repository in repository_dependency_tree: - debug_msg = "Appending revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + for required_repository_tup in repository_dependency_tups: + debug_msg = "Appending revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to all dependent repositories in installed_dependent_repositories_of_installed_repositories." log.debug( debug_msg ) - if required_repository.id in self.ids_of_installed_dependent_repositories_of_installed_repositories_keys: - for rd in self.installed_dependent_repositories_of_installed_repositories: - if rd.id == required_repository.id: - self.installed_dependent_repositories_of_installed_repositories[ rd ].append( repository ) - break + if required_repository_tup in self.installed_dependent_repositories_of_installed_repositories: + self.installed_dependent_repositories_of_installed_repositories[ required_repository_tup ].append( repository_tup ) else: - self.installed_dependent_repositories_of_installed_repositories[ required_repository ] = [ repository ] + self.installed_dependent_repositories_of_installed_repositories[ required_repository_tup ] = [ repository_tup ] def add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Add an entry to self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" - if tool_dependency.id not in self.ids_of_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies_keys: - debug_msg = "Adding an entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup not in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Adding an entry for version %s of %s %s " % ( version, type, name ) debug_msg += "to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." log.debug( debug_msg ) status = self.install_model.ToolDependency.installation_status.INSTALLED - installed_runtime_dependent_tool_dependencies = \ - tool_dependency_util.get_runtime_dependent_tool_dependencies( self.app, tool_dependency, status=status ) - self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency ] = \ - installed_runtime_dependent_tool_dependencies + installed_runtime_dependent_tool_dependency_tups = \ + tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=status ) + self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] = \ + installed_runtime_dependent_tool_dependency_tups def add_entry_to_installed_tool_dependencies_of_installed_repositories( self, repository ): """Add an entry to self.installed_tool_dependencies_of_installed_repositories.""" - if repository.id not in self.ids_of_installed_tool_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.installed_tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to installed_tool_dependencies_of_installed_repositories." log.debug( debug_msg ) - installed_tool_dependencies = [] - for td in repository.tool_dependencies: - if td.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: - installed_tool_dependencies.append( td ) - self.installed_tool_dependencies_of_installed_repositories[ repository ] = installed_tool_dependencies + installed_tool_dependency_tups = [] + for tool_dependency in repository.tool_dependencies: + if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + installed_tool_dependency_tups.append( tool_dependency_tup ) + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] = installed_tool_dependency_tups def add_entry_to_repository_dependencies_of_installed_repositories( self, repository ): """Add an entry to self.repository_dependencies_of_installed_repositories.""" - if repository.id not in self.ids_of_repository_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.repository_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to repository_dependencies_of_installed_repositories." log.debug( debug_msg ) - repository_dependency_tree = \ - repository_dependency_util.get_repository_dependency_tree_for_repository( self.app, - repository, - status=None ) - self.repository_dependencies_of_installed_repositories[ repository ] = repository_dependency_tree + repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=None ) + self.repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Add an entry to self.runtime_tool_dependencies_of_installed_tool_dependencies.""" - if tool_dependency.id not in self.ids_of_runtime_tool_dependencies_of_installed_tool_dependencies_keys: - debug_msg = "Adding an entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup not in self.runtime_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Adding an entry for version %s of %s %s " % ( version, type, name ) debug_msg += "to runtime_tool_dependencies_of_installed_tool_dependencies." log.debug( debug_msg ) - runtime_dependent_tool_dependencies = \ - tool_dependency_util.get_runtime_dependent_tool_dependencies( self.app, tool_dependency, status=None ) - self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency ] = \ - runtime_dependent_tool_dependencies + runtime_dependent_tool_dependency_tups = \ + tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=None ) + self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] = \ + runtime_dependent_tool_dependency_tups def add_entry_to_tool_dependencies_of_installed_repositories( self, repository ): """Add an entry to self.tool_dependencies_of_installed_repositories.""" - if repository.id not in self.ids_of_tool_dependencies_of_installed_repositories_keys: - debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) debug_msg += "to tool_dependencies_of_installed_repositories." log.debug( debug_msg ) - self.tool_dependencies_of_installed_repositories[ repository ] = repository.tool_dependencies + tool_dependency_tups = [] + for tool_dependency in repository.tool_dependencies: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + tool_dependency_tups.append( tool_dependency_tup ) + self.tool_dependencies_of_installed_repositories[ repository_tup ] = tool_dependency_tups - def get_containing_repository_for_tool_dependency( self, tool_dependency ): - for installed_repository, tool_dependencies in self.tool_dependencies_of_installed_repositories.items(): - td_ids = [ td.id for td in tool_dependencies ] - if tool_dependency.id in td_ids: - return installed_repository - return None + def get_containing_repository_for_tool_dependency( self, tool_dependency_tup ): + tool_shed_repository_id, name, version, type = tool_dependency_tup + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ).get( tool_shed_repository_id ) def get_repository_install_dir( self, tool_shed_repository ): for tool_config in self.tool_configs: @@ -176,9 +178,9 @@ relative_path = os.path.join( tool_path, ts, 'repos', - tool_shed_repository.owner, - tool_shed_repository.name, - tool_shed_repository.installed_changeset_revision ) + str( tool_shed_repository.owner ), + str( tool_shed_repository.name ), + str( tool_shed_repository.installed_changeset_revision ) ) if os.path.exists( relative_path ): return relative_path return None @@ -202,19 +204,18 @@ def handle_repository_uninstall( self, repository ): """Remove the dependency relationships for a repository that was just uninstalled.""" for tool_dependency in repository.tool_dependencies: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) # Remove this tool_dependency from all values in # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - for td, installed_runtime_dependent_tool_dependencies in \ + for td_tup, installed_runtime_dependent_tool_dependency_tups in \ self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items(): - irdtd_ids = [ irdtd.id for irdtd in installed_runtime_dependent_tool_dependencies ] - if td.id in irdtd_ids: - index = irdtd_ids[ td.id ] + if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups: # Remove the tool_dependency from the list. - del installed_runtime_dependent_tool_dependencies[ index ] + installed_runtime_dependent_tool_dependency_tups.remove( tool_dependency_tup ) # Add the possibly altered list to the altered dictionary. - altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td ] = \ - installed_runtime_dependent_tool_dependencies + altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td_tup ] = \ + installed_runtime_dependent_tool_dependency_tups self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = \ altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies. @@ -239,38 +240,12 @@ # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) # Populate self.installed_tool_dependencies_of_installed_repositories. - for r in self.installed_tool_dependencies_of_installed_repositories: - if r.id == repository.id: - self.installed_tool_dependencies_of_installed_repositories[ r ].append( tool_dependency ) - break - - @property - def ids_of_installed_dependent_repositories_of_installed_repositories_keys( self ): - return [ r.id for r in self.installed_dependent_repositories_of_installed_repositories.keys() ] - - @property - def ids_of_installed_repository_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.installed_repository_dependencies_of_installed_repositories.keys() ] - - @property - def ids_of_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies_keys( self ): - return [ td.id for td in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.keys() ] - - @property - def ids_of_installed_tool_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.installed_tool_dependencies_of_installed_repositories.keys() ] - - @property - def ids_of_repository_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.repository_dependencies_of_installed_repositories.keys() ] - - @property - def ids_of_runtime_tool_dependencies_of_installed_tool_dependencies_keys( self ): - return [ td.id for td in self.runtime_tool_dependencies_of_installed_tool_dependencies.keys() ] - - @property - def ids_of_tool_dependencies_of_installed_repositories_keys( self ): - return [ r.id for r in self.tool_dependencies_of_installed_repositories.keys() ] + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if repository_tup in self.installed_tool_dependencies_of_installed_repositories: + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ].append( tool_dependency_tup ) + else: + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] = [ tool_dependency_tup ] def load_dependency_relationships( self ): """Load relationships for all installed repositories and tool dependencies into in-memnory dictionaries.""" @@ -318,82 +293,76 @@ Remove an entry from self.installed_repository_dependencies_of_installed_repositories. A side-effect of this method is removal of appropriate value items from self.installed_dependent_repositories_of_installed_repositories. """ - # Remove this repository from value lists in self.installed_dependent_repositories_of_installed_repositories. - for r, v in self.installed_dependent_repositories_of_installed_repositories.items(): - rd_ids = [ rd.id for rd in v ] - if repository.id in rd_ids: + # Remove tuples defining this repository from value lists in self.installed_dependent_repositories_of_installed_repositories. + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_shed, name, owner, installed_changeset_revision = repository_tup + altered_installed_dependent_repositories_of_installed_repositories = {} + for r_tup, v_tups in self.installed_dependent_repositories_of_installed_repositories.items(): + if repository_tup in v_tups: debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + ( installed_changeset_revision, name, owner ) + r_tool_shed, r_name, r_owner, r_installed_changeset_revision = r_tup debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % \ - ( str( r.changeset_revision ), str( r.name ), str( r.owner ) ) + ( r_installed_changeset_revision, r_name, r_owner ) debug_msg += "in installed_repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) - new_v = [] - for rd in v: - if rd.id != repository.id: - new_v.append( rd ) - self.installed_dependent_repositories_of_installed_repositories[ r ] = new_v + log.debug( debug_msg ) + v_tups.remove( repository_tup ) + altered_installed_dependent_repositories_of_installed_repositories[ r_tup ] = v_tups + self.installed_dependent_repositories_of_installed_repositories = \ + altered_installed_dependent_repositories_of_installed_repositories # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories. - for r in self.installed_repository_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from installed_repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.installed_repository_dependencies_of_installed_repositories[ r ] - break + if repository_tup in self.installed_repository_dependencies_of_installed_repositories: + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from installed_repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.installed_repository_dependencies_of_installed_repositories[ repository_tup ] def remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Remove an entry from self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" - for td in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - if td.id == tool_dependency.id: - debug_msg = "Removing entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) - debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." - log.debug( debug_msg ) - del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td ] - break + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Removing entry for version %s of %s %s " % ( version, type, name ) + debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." + log.debug( debug_msg ) + del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] def remove_entry_from_installed_tool_dependencies_of_installed_repositories( self, repository ): """Remove an entry from self.installed_tool_dependencies_of_installed_repositories.""" - for r in self.installed_tool_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from installed_tool_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.installed_tool_dependencies_of_installed_repositories[ r ] - break + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.installed_tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from installed_tool_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] def remove_entry_from_repository_dependencies_of_installed_repositories( self, repository ): """Remove an entry from self.repository_dependencies_of_installed_repositories.""" - for r in self.repository_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.repository_dependencies_of_installed_repositories[ r ] - break + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.repository_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.repository_dependencies_of_installed_repositories[ repository_tup ] def remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): """Remove an entry from self.runtime_tool_dependencies_of_installed_tool_dependencies.""" - for td in self.runtime_tool_dependencies_of_installed_tool_dependencies: - if td.id == tool_dependency.id: - debug_msg = "Removing entry for version %s of %s %s " % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) - debug_msg += "from runtime_tool_dependencies_of_installed_tool_dependencies." - log.debug( debug_msg ) - del self.runtime_tool_dependencies_of_installed_tool_dependencies[ td ] - break + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup in self.runtime_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Removing entry for version %s of %s %s from runtime_tool_dependencies_of_installed_tool_dependencies." % \ + ( version, type, name ) + log.debug( debug_msg ) + del self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] def remove_entry_from_tool_dependencies_of_installed_repositories( self, repository ): """Remove an entry from self.tool_dependencies_of_installed_repositories.""" - for r in self.tool_dependencies_of_installed_repositories: - if r.id == repository.id: - debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) - debug_msg += "from tool_dependencies_of_installed_repositories." - log.debug( debug_msg ) - del self.tool_dependencies_of_installed_repositories[ r ] - break + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s from tool_dependencies_of_installed_repositories." % \ + ( installed_changeset_revision, name, owner ) + log.debug( debug_msg ) + del self.tool_dependencies_of_installed_repositories[ repository_tup ] diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r f2731f3baec83e5ebf038ac703164b3f4ee53a72 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -71,8 +71,8 @@ def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): """ - Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined - by the received repo_info_dict. + Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated + with the repository defined by the received repo_info_dict. """ repository = None installed_rd = {} @@ -102,7 +102,8 @@ # Discover all repository dependencies and retrieve information for installing them. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) - has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) + has_repository_dependencies_only_if_compiling_contained_td = \ + all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) @@ -138,7 +139,8 @@ # We have a single repository with (possibly) no defined repository dependencies. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) - has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) + has_repository_dependencies_only_if_compiling_contained_td = \ + all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) @@ -202,8 +204,8 @@ # Get the description from the metadata in case it has a value. repository_dependencies = metadata.get( 'repository_dependencies', {} ) description = repository_dependencies.get( 'description', None ) - # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the missing_repository_dependencies - # dictionaries for proper display parsing. + # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the + # missing_repository_dependencies dictionaries for proper display parsing. root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, repository.name, repository.owner, diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r f2731f3baec83e5ebf038ac703164b3f4ee53a72 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 @@ -375,22 +375,32 @@ all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies ) return all_repository_dependencies -def get_repository_dependency_tree_for_repository( app, repository, dependency_tree=None, status=None ): +def get_repository_dependency_tups_for_repository( app, repository, dependency_tups=None, status=None ): """ - Return a list of of tool_shed_repository ids (whose status can be anything) required by the received repository. The - returned list defines the entire repository dependency tree. + Return a list of of tuples defining tool_shed_repository objects (whose status can be anything) required by the + received repository. The returned list defines the entire repository dependency tree. """ - if dependency_tree is None: - dependency_tree = [] - tree_object_ids = [ r.id for r in dependency_tree ] + if dependency_tups is None: + dependency_tups = [] + repository_tup = get_repository_tuple_for_installed_repository_manager( repository ) for rrda in repository.required_repositories: repository_dependency = rrda.repository_dependency required_repository = repository_dependency.repository if status is None or required_repository.status == status: - if required_repository.id not in tree_object_ids: - dependency_tree.append( required_repository ) - return get_repository_dependency_tree_for_repository( app, required_repository, dependency_tree=dependency_tree ) - return dependency_tree + required_repository_tup = get_repository_tuple_for_installed_repository_manager( required_repository ) + if required_repository_tup == repository_tup: + # We have a circular repository dependency relationship, skip this entry. + continue + if required_repository_tup not in dependency_tups: + dependency_tups.append( required_repository_tup ) + return get_repository_dependency_tups_for_repository( app, required_repository, dependency_tups=dependency_tups ) + return dependency_tups + +def get_repository_tuple_for_installed_repository_manager( repository ): + return ( str( repository.tool_shed ), + str( repository.name ), + str( repository.owner ), + str( repository.installed_changeset_revision ) ) def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ): updated_key_rd_dicts = [] @@ -402,9 +412,10 @@ if suc.tool_shed_is_this_tool_shed( rd_toolshed ): repository = suc.get_repository_by_name_and_owner( trans.app, rd_name, rd_owner ) if repository: - repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, - trans.security.encode_id( repository.id ), - rd_changeset_revision ) + repository_metadata = \ + metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + trans.security.encode_id( repository.id ), + rd_changeset_revision ) if repository_metadata: # The repository changeset_revision is installable, so no updates are available. new_key_rd_dict = {} diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r f2731f3baec83e5ebf038ac703164b3f4ee53a72 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 @@ -200,30 +200,6 @@ tool_dependency_definition_type_class.label return message -def get_runtime_dependent_tool_dependencies( app, tool_dependency, status=None ): - """ - Return the list of tool dependency objects that require the received tool dependency at run time. The returned - list will be filtered by the received status if it is not None. This method is called only from Galaxy. - """ - runtime_dependent_tool_dependencies = [] - required_env_shell_file_path = tool_dependency.get_env_shell_file_path( app ) - if required_env_shell_file_path: - required_env_shell_file_path = os.path.abspath( required_env_shell_file_path ) - if required_env_shell_file_path is not None: - for td in app.install_model.context.query( app.install_model.ToolDependency ): - if status is None or td.status == status: - env_shell_file_path = td.get_env_shell_file_path( app ) - if env_shell_file_path is not None: - try: - contents = open( env_shell_file_path, 'r' ).read() - except Exception, e: - contents = None - log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % \ - ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) - if contents is not None and contents.find( required_env_shell_file_path ) >= 0: - runtime_dependent_tool_dependencies.append( td ) - return runtime_dependent_tool_dependencies - def get_download_url_for_platform( url_templates, platform_info_dict ): ''' Compare the dict returned by get_platform_info() with the values specified in the url_template element. Return @@ -322,6 +298,31 @@ env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) return env_sh_file_path +def get_runtime_dependent_tool_dependency_tuples( app, tool_dependency, status=None ): + """ + Return the list of tool dependency objects that require the received tool dependency at run time. The returned + list will be filtered by the received status if it is not None. This method is called only from Galaxy. + """ + runtime_dependent_tool_dependency_tups = [] + required_env_shell_file_path = tool_dependency.get_env_shell_file_path( app ) + if required_env_shell_file_path: + required_env_shell_file_path = os.path.abspath( required_env_shell_file_path ) + if required_env_shell_file_path is not None: + for td in app.install_model.context.query( app.install_model.ToolDependency ): + if status is None or td.status == status: + env_shell_file_path = td.get_env_shell_file_path( app ) + if env_shell_file_path is not None: + try: + contents = open( env_shell_file_path, 'r' ).read() + except Exception, e: + contents = None + log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % \ + ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) + if contents is not None and contents.find( required_env_shell_file_path ) >= 0: + td_tuple = get_tool_dependency_tuple_for_installed_repository_manager( td ) + runtime_dependent_tool_dependency_tups.append( td_tuple ) + return runtime_dependent_tool_dependency_tups + def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.install_model.context.query( trans.install_model.ToolDependency ).get( trans.security.decode_id( id ) ) @@ -386,6 +387,13 @@ repository_name, repository_changeset_revision ) ) +def get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ): + if tool_dependency.type is None: + type = None + else: + type = str( tool_dependency.type ) + return ( tool_dependency.tool_shed_repository_id, str( tool_dependency.name ), str( tool_dependency.version ), type ) + def handle_tool_dependency_installation_error( app, tool_dependency, error_message, remove_installation_path=False ): # Since there was an installation error, remove the installation directory because the install_package method uses # this: "if os.path.exists( install_dir ):". Setting remove_installation_path to True should rarely occur. It is diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r f2731f3baec83e5ebf038ac703164b3f4ee53a72 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -54,32 +54,27 @@ %endif %if not can_uninstall_repository: <% + from tool_shed.util.repository_dependency_util import get_repository_tuple_for_installed_repository_manager + from tool_shed.util.tool_dependency_util import get_tool_dependency_tuple_for_installed_repository_manager + irm = trans.app.installed_repository_manager + repository_tup = get_repository_tuple_for_installed_repository_manager( repository ) # Get installed repositories that this repository requires. installed_dependent_repositories = [] installed_runtime_dependent_tool_dependencies = [] - for r in irm.installed_dependent_repositories_of_installed_repositories: - if r.id == repository.id: - installed_dependent_repositories = irm.installed_dependent_repositories_of_installed_repositories[ r ] - break + installed_dependent_repositories = irm.installed_dependent_repositories_of_installed_repositories.get( repository_tup, [] ) # Get this repository's installed tool dependencies. - installed_tool_dependencies = [] - for r in irm.installed_tool_dependencies_of_installed_repositories: - if r.id == repository.id: - installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories[ r ] - break + installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories.get( repository_tup, [] ) # Get installed runtime dependent tool dependencies of this repository's installed tool dependencies. installed_runtime_dependent_tool_dependencies = [] - for itd in installed_tool_dependencies: - for td in irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - if td.id == itd.id: - installed_dependent_tds = \ - irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td ] - if installed_dependent_tds: - installed_runtime_dependent_tool_dependencies.extend( installed_dependent_tds ) + for itd_tup in installed_tool_dependencies: + installed_dependent_td_tups = \ + irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.get( itd_tup, [] ) + if installed_dependent_td_tups: + installed_runtime_dependent_tool_dependencies.extend( installed_dependent_td_tups ) %> %if installed_dependent_repositories or installed_runtime_dependent_tool_dependencies: <table width="100%" border="0" cellpadding="0" cellspacing="0"> @@ -92,29 +87,28 @@ %if installed_dependent_repositories: <label>Dependent repositories:</label><ul> - %for installed_dependent_repository in installed_dependent_repositories: + %for installed_dependent_repository_tup in installed_dependent_repositories: <% - changeset_revision = installed_dependent_repository.changeset_revision - name = installed_dependent_repository.name - owner = installed_dependent_repository.owner + tool_shed, name, owner, installed_changeset_revision, status = installed_dependent_repository_tup %> - <li>Revision <b>${ changeset_revision | h}</b> of repository <b>${name | h}</b> owned by <b>${owner | h}</b></li> + <li>Revision <b>${ installed_changeset_revision | h}</b> of repository <b>${name | h}</b> owned by <b>${owner | h}</b></li> %endfor </ul> %endif %if installed_runtime_dependent_tool_dependencies: <label>Runtime dependent tool dependencies of this repository's tool dependencies:</label><ul> - %for td in installed_runtime_dependent_tool_dependencies: + %for td_tup in installed_runtime_dependent_tool_dependencies: <% - containing_repository = irm.get_containing_repository_for_tool_dependency( td ) + tool_shed_repository_id, name, version, type, status = td_tup + containing_repository = irm.get_containing_repository_for_tool_dependency( td_tup ) repository_name = containing_repository.name changeset_revision = containing_repository.changeset_revision owner = containing_repository.owner %><li> - Version <b>${td.version}</b> of ${td.type} <b>${td.name}</b> contained in revision - <b>${changeset_revision | h}</b> of repository <b>${repository_name | h}</b> owned by <b>${owner}</b> + Version <b>${version | h}</b> of ${type | h} <b>${name | h}</b> contained in revision + <b>${changeset_revision | h}</b> of repository <b>${repository_name | h}</b> owned by <b>${owner | h}</b></li> %endfor </ul> diff -r 9fa11fc0e2751d232dcf09265d778a6e221c756f -r f2731f3baec83e5ebf038ac703164b3f4ee53a72 templates/admin/tool_shed_repository/repository_actions_menu.mako --- a/templates/admin/tool_shed_repository/repository_actions_menu.mako +++ b/templates/admin/tool_shed_repository/repository_actions_menu.mako @@ -30,7 +30,6 @@ <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a> - <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ) )}">Repair repository</a> %if repository.can_reset_metadata: <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='reset_repository_metadata', id=trans.security.encode_id( repository.id ) )}">Reset repository metadata</a> %endif @@ -42,6 +41,7 @@ %endif <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a> %endif + <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ) )}">Repair repository</a></div></ul></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Improve language for workflow outputs tooltip.
by commits-noreply＠bitbucket.org 13 Dec '13

13 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9fa11fc0e275/ Changeset: 9fa11fc0e275 User: jgoecks Date: 2013-12-13 16:00:20 Summary: Improve language for workflow outputs tooltip. Affected #: 1 file diff -r b3eeedb81a1e0db8d643af0cbba68f55eb49cdb0 -r 9fa11fc0e2751d232dcf09265d778a6e221c756f static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -360,7 +360,7 @@ workflow.has_changes = true; canvas_manager.draw_overview(); }))) - .tooltip({delay:500, title: "Flag this as a workflow output. All non-flagged outputs will be hidden." }); + .tooltip({delay:500, title: "Mark dataset as a workflow output. All unmarked datasets will be hidden." }); callout.css({ top: '50%', margin:'-8px 0px 0px 0px', 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: 3 new changesets
by commits-noreply＠bitbucket.org 12 Dec '13

12 Dec '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3fe8dd26c25/ Changeset: e3fe8dd26c25 User: jmchilton Date: 2013-12-13 06:24:15 Summary: casperjs: PEP-8 fixes for casperjs_runner.py. Affected #: 1 file diff -r e307768aa1f3a05b4222900df1047bf5d1488003 -r e3fe8dd26c2541d89126a783b954727ef277f620 test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -18,7 +18,7 @@ import sys ( major, minor, micro, releaselevel, serial ) = sys.version_info if minor < 6: - msg = 'casperjs requires python 2.6 or newer. Using: %s' %( sys.version ) + msg = 'casperjs requires python 2.6 or newer. Using: %s' % ( sys.version ) try: # if nose is installed do a skip test from nose.plugins.skip import SkipTest @@ -36,7 +36,6 @@ import unittest from server_env import TestEnvironment -import pprint import logging logging.basicConfig( stream=sys.stderr, name=__name__ ) log = logging.getLogger( __name__ ) @@ -50,12 +49,14 @@ better way to turn debugging on from the environment """ + # ==================================================================== class HeadlessJSJavascriptError( Exception ): """An error that occurrs in the javascript test file. """ pass + class CasperJSTestCase( unittest.TestCase ): """Casper tests running in a unittest framework. """ @@ -76,7 +77,7 @@ casper_done_str = '# Stopping' # convert js test results to unittest.TestResults - results_adapter = None #CasperJsonToUnittestResultsConverter() + results_adapter = None # CasperJsonToUnittestResultsConverter() # ---------------------------------------------------------------- run the js script def run_js_script( self, rel_script_path, *args, **kwargs ): @@ -166,14 +167,14 @@ """Converts the headless' error from JSON into a more informative python HeadlessJSJavascriptError. """ - get_error = lambda d: d[ 'errors' ][0] - get_msg = lambda err: err[ 'msg' ] - get_trace = lambda err: err[ 'backtrace' ] + get_error = lambda d: d[ 'errors' ][0] + get_msg = lambda err: err[ 'msg' ] + get_trace = lambda err: err[ 'backtrace' ] try: # assume it's json and located in errors (and first) js_test_results = json.loads( stdout_output ) last_error = get_error( js_test_results ) - err_string = ( "%s\n%s" %( get_msg( last_error ), + err_string = ( "%s\n%s" % ( get_msg( last_error ), self.browser_backtrace_to_string( get_trace( last_error ) ) ) ) # if we couldn't parse json from what's returned on the error, dump stdout @@ -187,7 +188,7 @@ except Exception, exc: log.debug( '(failed to parse error returned from %s: %s)', _PATH_TO_HEADLESS, str( exc ) ) return HeadlessJSJavascriptError( - "ERROR in headless browser script %s" %( script_path ) ) + "ERROR in headless browser script %s" % ( script_path ) ) # otherwise, raise with msg and backtrace return HeadlessJSJavascriptError( err_string ) @@ -196,10 +197,10 @@ """Converts list of trace dictionaries (as might be returned from json results) to a string similar to a python backtrace. """ - template = ' File "%s", line %s, in %s' + template = ' File "%s", line %s, in %s' traces = [] for trace in backtrace: - traces.append( template %( trace[ 'file' ], trace[ 'line' ], trace[ 'function' ] ) ) + traces.append( template % ( trace[ 'file' ], trace[ 'line' ], trace[ 'function' ] ) ) return '\n'.join( traces ) # ---------------------------------------------------------------- results @@ -216,7 +217,7 @@ js_test_results = json.loads( results ) failures = js_test_results[ 'testResults' ][ 'failures' ] assert len( failures ) == 0, ( - "%d assertions failed in the headless browser tests" %( len( failures ) ) + "%d assertions failed in the headless browser tests" % ( len( failures ) ) + " (see the log for details)" ) # ---------------------------------------------------------------- TestCase overrides @@ -247,7 +248,7 @@ """ results_dict = json.loads( json_results ) failures = results_dict[ 'testResults' ][ 'failures' ] - passes = results_dict[ 'testResults' ][ 'passes' ] + passes = results_dict[ 'testResults' ][ 'passes' ] self.add_json_failures_to_results( failures, test ) self.add_json_successes_to_results( passes, test ) @@ -271,11 +272,11 @@ """ #TODO: this is all too elaborate fail_type = casper_failure[ 'type' ] - values = json.dumps( casper_failure[ 'values' ] ) - desc = casper_failure[ 'standard' ] + values = json.dumps( casper_failure[ 'values' ] ) + desc = casper_failure[ 'standard' ] if 'messgae' in casper_failure: - desc = capser_failure[ 'message' ] - failure_msg = "(%s) %s: %s" %( fail_type, desc, values ) + desc = casper_failure[ 'message' ] + failure_msg = "(%s) %s: %s" % ( fail_type, desc, values ) #TODO: tb is empty ([]) - can we get file info from casper, covert to py trace? return ( failure_class, failure_msg, [] ) @@ -295,6 +296,7 @@ def setup_module(): log.debug( '\n--------------- setting up module' ) + def teardown_module(): log.debug( '\n--------------- tearing down module' ) @@ -304,6 +306,7 @@ 'password': '123456' } + # ==================================================================== TESTCASE EXAMPLE # these could be broken out into other py files - shouldn't be necc. ATM class Test_01_User( CasperJSTestCase ): https://bitbucket.org/galaxy/galaxy-central/commits/4f2a368ff1ab/ Changeset: 4f2a368ff1ab User: jmchilton Date: 2013-12-13 06:24:15 Summary: casperjs: Fixes for admin checking. Masthead link changed in recent commit. Tweak config file parsing to handle spaces between e-mail addresses. Affected #: 2 files diff -r e3fe8dd26c2541d89126a783b954727ef277f620 -r 4f2a368ff1ab2739c396f4e56e29d8664806dc0b test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -207,7 +207,7 @@ // check for the setting in sg and the universe_wsgi.ini file var adminData = this.spaceghost.options.adminUser, iniAdminEmails = this.spaceghost.getUniverseSetting( 'admin_users' ); - iniAdminEmails = ( iniAdminEmails )?( iniAdminEmails.split( ',' ) ):( null ); + iniAdminEmails = ( iniAdminEmails )?( iniAdminEmails.split( ',' ).map( function( email ) { return email.trim(); } ) ):( null ); //TODO: seems like we only need the wsgi setting - that's the only thing we can't change if( adminData ){ diff -r e3fe8dd26c2541d89126a783b954727ef277f620 -r 4f2a368ff1ab2739c396f4e56e29d8664806dc0b test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -1129,7 +1129,7 @@ }, masthead : { - adminLink : '#masthead a[href="/admin"]', + adminLink : '#masthead a[href="/admin/index"]', userMenu : { userEmail : 'a #user-email', userEmail_xpath : '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' https://bitbucket.org/galaxy/galaxy-central/commits/b3eeedb81a1e/ Changeset: b3eeedb81a1e User: jmchilton Date: 2013-12-13 06:24:15 Summary: casperjs: Add some notes. Affected #: 1 file diff -r 4f2a368ff1ab2739c396f4e56e29d8664806dc0b -r b3eeedb81a1e0db8d643af0cbba68f55eb49cdb0 test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -13,6 +13,16 @@ * casperjs usertests.js --url='http://localhost:8080' --verbose=true --logLevel=debug (see casperjs.org for more information) + +Note: This seems to not work with CasperJS 1.1 (and PhantomJS 1.9) - Casper 1.0.xx and +PhantomJS 1.8 work for me (John). + +Note: Example of specifing user and admin user credentials. + +casperjs api-configuration-tests.js --url="http://localhost:8080" \ + --admin='{"email": "foo(a)example.com", "password": "123456" }' \ + '{ "testUser": { "email": "foo(a)example.com", "password": "123456" } }' + """ # -------------------------------------------------------------------- can't do 2.5 import sys Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: persist open state of search, tag, and annotation UIs
by commits-noreply＠bitbucket.org 12 Dec '13

12 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e307768aa1f3/ Changeset: e307768aa1f3 User: carlfeberhard Date: 2013-12-12 23:10:30 Summary: History panel: persist open state of search, tag, and annotation UIs Affected #: 2 files diff -r 4241eff3f67c3d42fe51564c52aafabf65cc6130 -r e307768aa1f3a05b4222900df1047bf5d1488003 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -7,9 +7,32 @@ // ============================================================================ +/** session storage for history panel preferences (and to maintain state) + */ +var HistoryPanelPrefs = SessionStorageModel.extend({ + defaults : { + /** is the panel currently showing the search/filter controls? */ + searching : false, + /** should the tags editor be shown or hidden initially? */ + tagsEditorShown : false, + /** should the annotation editor be shown or hidden initially? */ + annotationEditorShown : false + }, + toString : function(){ + return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')'; + } +}); + +/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */ +HistoryPanelPrefs.storageKey = function storageKey(){ + return ( 'history-panel' ); +}; + + +// ============================================================================ /** session storage for individual history preferences */ -var HistoryPanelPrefs = SessionStorageModel.extend({ +var HistoryPrefs = SessionStorageModel.extend({ defaults : { //TODO:?? expandedHdas to array? expandedHdas : {}, @@ -27,15 +50,15 @@ this.save( 'expandedHdas', _.omit( this.get( 'expandedHdas' ), id ) ); }, toString : function(){ - return 'HistoryPanelPrefs(' + this.id + ')'; + return 'HistoryPrefs(' + this.id + ')'; } }); /** key string to store each histories settings under */ -HistoryPanelPrefs.historyStorageKey = function historyStorageKey( historyId ){ +HistoryPrefs.historyStorageKey = function historyStorageKey( historyId ){ // class lvl for access w/o instantiation if( !historyId ){ - throw new Error( 'HistoryPanelPrefs.historyStorageKey needs valid id: ' + historyId ); + throw new Error( 'HistoryPrefs.historyStorageKey needs valid id: ' + historyId ); } // single point of change return ( 'history:' + historyId ); @@ -109,28 +132,30 @@ this.log( this + '.initialize:', attributes ); // ---- set up instance vars + // control contents/behavior based on where (and in what context) the panel is being used /** which backbone view class to use when displaying the hda list */ this.HDAViewClass = attributes.HDAViewClass || this.defaultHDAViewClass; /** where should pages from links be displayed? (default to new tab/window) */ this.linkTarget = attributes.linkTarget || '_blank'; + // ---- sub views and saved elements /** map of hda model ids to hda views */ this.hdaViews = {}; /** loading indicator */ this.indicator = new LoadingIndicator( this.$el ); + // ---- persistent state and preferences + /** maintain state / preferences over page loads */ + this.preferences = new HistoryPanelPrefs( _.extend({ + id : HistoryPanelPrefs.storageKey() + }, _.pick( attributes, _.keys( HistoryPanelPrefs.prototype.defaults ) ))); + /** filters for displaying hdas */ this.filters = []; -//TODO: move to storage and persist - /** is the panel currently showing the search/filter controls? */ - this.searching = attributes.searching || false; + // states/modes the panel can be in /** is the panel currently showing the dataset selection controls? */ this.selecting = attributes.selecting || false; - - /** should the tags editor be shown or hidden initially? */ - this.tagsEditorShown = attributes.tagsShown || false; - /** should the tags editor be shown or hidden initially? */ this.annotationEditorShown = attributes.annotationEditorShown || false; this._setUpListeners(); @@ -397,8 +422,8 @@ */ _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){ //console.debug( '_setUpWebStorage', initiallyExpanded, show_deleted, show_hidden ); - this.storage = new HistoryPanelPrefs({ - id: HistoryPanelPrefs.historyStorageKey( this.model.get( 'id' ) ) + this.storage = new HistoryPrefs({ + id: HistoryPrefs.historyStorageKey( this.model.get( 'id' ) ) }); // expanded Hdas is a map of hda.ids -> a boolean repr'ing whether this hda's body is already expanded @@ -436,7 +461,7 @@ return ( this.storage )?( this.storage.get() ):( {} ); } //TODO: make storage engine generic - var item = sessionStorage.getItem( HistoryPanelPrefs.historyStorageKey( historyId ) ); + var item = sessionStorage.getItem( HistoryPrefs.historyStorageKey( historyId ) ); return ( item === null )?( {} ):( JSON.parse( item ) ); }, @@ -525,6 +550,7 @@ panel.$el.empty(); if( $newRender ){ panel.$el.append( $newRender.children() ); + panel.renderBasedOnPrefs(); } next(); }, @@ -581,6 +607,12 @@ return $newRender; }, + renderBasedOnPrefs : function(){ + if( this.preferences.get( 'searching' ) ){ + this.showSearchControls( 0 ); + } + }, + _renderTags : function( $where ){ var panel = this; this.tagsEditor = new TagsEditor({ @@ -589,11 +621,11 @@ onshowFirstTime : function(){ this.render(); }, // show hide hda view tag editors when this is shown/hidden onshow : function(){ - panel.tagsEditorShown = true; + panel.preferences.set( 'tagsEditorShown', true ); panel.toggleHDATagEditors( true, panel.fxSpeed ); }, onhide : function(){ - panel.tagsEditorShown = false; + panel.preferences.set( 'tagsEditorShown', false ); panel.toggleHDATagEditors( false, panel.fxSpeed ); }, $activator : faIconButton({ @@ -602,6 +634,9 @@ faIcon : 'fa-tags' }).appendTo( $where.find( '.history-secondary-actions' ) ) }); + if( this.preferences.get( 'tagsEditorShown' ) ){ + this.tagsEditor.toggle( true ); + } }, _renderAnnotation : function( $where ){ var panel = this; @@ -611,11 +646,11 @@ onshowFirstTime : function(){ this.render(); }, // show hide hda view annotation editors when this is shown/hidden onshow : function(){ - panel.annotationEditorShown = true; + panel.preferences.set( 'annotationEditorShown', true ); panel.toggleHDAAnnotationEditors( true, panel.fxSpeed ); }, onhide : function(){ - panel.annotationEditorShown = false; + panel.preferences.set( 'annotationEditorShown', false ); panel.toggleHDAAnnotationEditors( false, panel.fxSpeed ); }, $activator : faIconButton({ @@ -624,6 +659,9 @@ faIcon : 'fa-comment' }).appendTo( $where.find( '.history-secondary-actions' ) ) }); + if( this.preferences.get( 'annotationEditorShown' ) ){ + this.annotationEditor.toggle( true ); + } }, /** button for opening search */ _renderSearchButton : function( $where ){ @@ -759,8 +797,8 @@ linkTarget : this.linkTarget, expanded : expanded, //draggable : true, - tagsEditorShown : this.tagsEditorShown, - annotationEditorShown : this.annotationEditorShown, + tagsEditorShown : this.preferences.get( 'tagsEditorShown' ), + annotationEditorShown : this.preferences.get( 'annotationEditorShown' ), selectable : this.selecting, hasUser : this.model.ownedByCurrUser(), logger : this.logger @@ -979,22 +1017,38 @@ onclear : onSearchClear }); }, - - /** toggle showing/hiding the search controls (rendering first on the initial show) */ - toggleSearchControls : function(){ - var $searchControls = this.$el.find( '.history-search-controls' ); +//TODO: to hidden/shown plugin + showSearchControls : function( speed ){ + speed = ( speed === undefined )?( this.fxSpeed ):( speed ); + var panel = this, + $searchControls = this.$el.find( '.history-search-controls' ); + // if it hasn't been rendered - do it now if( !$searchControls.children().size() ){ $searchControls = this.renderSearchControls( $searchControls ).hide(); } - $searchControls.slideToggle( this.fxSpeed, function(){ - if( $( this ).is( ':visible' ) ){ - this.searching = true; - $( this ).find( 'input' ).focus(); - } else { - this.searching = false; - } + // then slide open, focusing on the input, and persisting the setting when it's done + $searchControls.show( speed, function(){ + $( this ).find( 'input' ).focus(); + panel.preferences.set( 'searching', true ); }); }, + hideSearchControls : function(){ + speed = ( speed === undefined )?( this.fxSpeed ):( speed ); + var panel = this; + this.$el.find( '.history-search-controls' ).hide( speed, function(){ + panel.preferences.set( 'searching', false ); + }); + }, + + /** toggle showing/hiding the search controls (rendering first on the initial show) */ + toggleSearchControls : function( eventOrSpeed ){ + speed = ( jQuery.type( eventOrSpeed ) === 'number' )?( eventOrSpeed ):( this.fxSpeed ); + if( this.$el.find( '.history-search-controls' ).is( ':visible' ) ){ + this.hideSearchControls( speed ); + } else { + this.showSearchControls( speed ); + } + }, // ........................................................................ multi-select of hdas showSelectors : function( speed ){ diff -r 4241eff3f67c3d42fe51564c52aafabf65cc6130 -r e307768aa1f3a05b4222900df1047bf5d1488003 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(g,d,b,a){var c=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(h){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([h],[true])))},removeExpandedHda:function(h){this.save("expandedHdas",_.omit(this.get("expandedHdas"),h))},toString:function(){return"HistoryPanelPrefs("+this.id+")"}});c.historyStorageKey=function f(h){if(!h){throw new Error("HistoryPanelPrefs.historyStorageKey needs valid id: "+h)}return("history:"+h)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(h){h=h||{};if(h.logger){this.logger=h.logger}this.log(this+".initialize:",h);this.HDAViewClass=h.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=h.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];this.searching=h.searching||false;this.selecting=h.selecting||false;this.tagsEditorShown=h.tagsShown||false;this.annotationEditorShown=h.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers()}if(h.onready){h.onready.call(this)}},_setUpListeners:function(){this.on("error",function(i,l,h,k,j){this.errorHandler(i,l,h,k,j)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(h){this.log(this+"",arguments)},this)}},errorHandler:function(j,m,i,l,k){var h=this._parseErrorMessage(j,m,i,l,k);if(m&&m.status===0&&m.readyState===0){}else{if(m&&m.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",h.message,h.details)})}else{this.displayMessage("error",h.message,h.details)}}}},_parseErrorMessage:function(k,o,j,n,m){var i=Galaxy.currUser,h={message:this._bePolite(n),details:{user:(i instanceof User)?(i.toJSON()):(i+""),source:(k instanceof Backbone.Model)?(k.toJSON()):(k+""),xhr:o,options:(o)?(_.omit(j,"xhr")):(j)}};_.extend(h.details,m||{});if(o&&_.isFunction(o.getAllResponseHeaders)){var l=o.getAllResponseHeaders();l=_.compact(l.split("\n"));l=_.map(l,function(p){return p.split(": ")});h.details.xhr.responseHeaders=_.object(l)}return h},_bePolite:function(h){h=h||_l("An error occurred while getting updates from the server");return h+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(i){var h=this;return this.loadHistoryWithHDADetails("current",i).then(function(k,j){h.trigger("current-history",h)})},switchToHistory:function(k,j){var h=this,i=function(){return jQuery.post(galaxy_config.root+"api/histories/"+k+"/set_as_current")};return this.loadHistoryWithHDADetails(k,j,i).then(function(m,l){h.trigger("switched-history",h)})},createNewHistory:function(j){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var h=this,i=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,j,i).then(function(l,k){h.trigger("new-history",h)})},loadHistoryWithHDADetails:function(k,j,i,m){var h=this,l=function(n){return h.getExpandedHdaIds(n.id)};return this.loadHistory(k,j,i,m,l)},loadHistory:function(k,j,i,n,l){this.trigger("loading-history",this);j=j||{};var h=this;var m=g.History.getHistoryData(k,{historyFn:i,hdaFn:n,hdaDetailIds:j.initiallyExpanded||l});return this._loadHistoryFromXHR(m,j).fail(function(q,o,p){h.trigger("error",h,q,j,_l("An error was encountered while "+o),{historyId:k,history:p||{}})}).always(function(){h.trigger("loading-done",h)})},_loadHistoryFromXHR:function(j,i){var h=this;j.then(function(k,l){h.setModel(k,l,i)});j.fail(function(l,k){h.render()});return j},setModel:function(j,h,i){i=i||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){j.user=Galaxy.currUser.toJSON()}this.model=new g.History(j,h,i);this._setUpWebStorage(i.initiallyExpanded,i.show_deleted,i.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(i,h,j){this.storage=new c({id:c.historyStorageKey(this.model.get("id"))});if(_.isObject(i)){this.storage.set("exandedHdas",i)}if(_.isBoolean(h)){this.storage.set("show_deleted",h)}if(_.isBoolean(j)){this.storage.set("show_hidden",j)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var h in sessionStorage){if(h.indexOf("history:")===0){sessionStorage.removeItem(h)}}},getStoredOptions:function(i){if(!i||i==="current"){return(this.storage)?(this.storage.get()):({})}var h=sessionStorage.getItem(c.historyStorageKey(i));return(h===null)?({}):(JSON.parse(h))},getExpandedHdaIds:function(h){var i=this.getStoredOptions(h).expandedHdas;return((_.isEmpty(i))?([]):(_.keys(i)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(i,k,h,j){this.errorHandler(i,k,h,j)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(h){this.model.fetch()},this);this.model.hdas.on("state:ready",function(i,j,h){if((!i.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[i.id])}},this)},render:function(j,k){j=(j===undefined)?(this.fxSpeed):(j);var h=this,i;if(this.model){i=this.renderModel()}else{i=this.renderWithoutModel()}$(h).queue("fx",[function(l){if(j&&h.$el.is(":visible")){h.$el.fadeOut(j,l)}else{l()}},function(l){h.$el.empty();if(i){h.$el.append(i.children())}l()},function(l){if(j&&!h.$el.is(":visible")){h.$el.fadeIn(j,l)}else{l()}},function(l){if(k){k.call(this)}h.trigger("rendered",this);l()}]);return this},renderWithoutModel:function(){var h=$("<div/>"),i=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return h.append(i)},renderModel:function(){var h=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){h.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{h.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(h);this._renderAnnotation(h)}}h.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(h);this.renderHdas(h);return h},_renderTags:function(h){var i=this;this.tagsEditor=new TagsEditor({model:this.model,el:h.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.tagsEditorShown=true;i.toggleHDATagEditors(true,i.fxSpeed)},onhide:function(){i.tagsEditorShown=false;i.toggleHDATagEditors(false,i.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".history-secondary-actions"))})},_renderAnnotation:function(h){var i=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:h.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.annotationEditorShown=true;i.toggleHDAAnnotationEditors(true,i.fxSpeed)},onhide:function(){i.annotationEditorShown=false;i.toggleHDAAnnotationEditors(false,i.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".history-secondary-actions"))})},_renderSearchButton:function(h){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(h){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(h){h=h||this.$el;h.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var i=this;h.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(j){h.find(".history-name").text(j);i.model.save({name:j}).fail(function(){h.find(".history-name").text(i.model.previous("name"))})}});this._setUpDatasetActionsPopup(h)},_setUpDatasetActionsPopup:function(h){var i=this;(new PopupMenu(h.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.hide;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Unhide datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.unhide;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Delete datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype["delete"];i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Undelete datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.undelete;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var j=d.HistoryDatasetAssociation.prototype.purge;i.getSelectedHdaCollection().ajaxQueue(j)}}}]))},refreshHdas:function(i,h){if(this.model){return this.model.refresh(i,h)}return $.when()},addHdaView:function(k){this.log("add."+this,k);var i=this;if(!k.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function j(m){var l=i.$el.find(i.emptyMsgSelector);if(l.is(":visible")){l.fadeOut(i.fxSpeed,m)}else{m()}},function h(m){i.scrollToTop();var l=i.$el.find(i.datasetsSelector);i.createHdaView(k).$el.hide().prependTo(l).slideDown(i.fxSpeed)}])},createHdaView:function(j){var i=j.get("id"),h=this.storage.get("expandedHdas")[i],k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:h,tagsEditorShown:this.tagsEditorShown,annotationEditorShown:this.annotationEditorShown,selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(k);this.hdaViews[i]=k;return k.render()},_setUpHdaListeners:function(i){var h=this;i.on("body-expanded",function(j){h.storage.addExpandedHda(j)});i.on("body-collapsed",function(j){h.storage.removeExpandedHda(j)});i.on("error",function(k,m,j,l){h.errorHandler(k,m,j,l)})},handleHdaDeletionChange:function(h){if(h.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[h.id])}},handleHdaVisibleChange:function(h){if(h.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[h.id])}},removeHdaView:function(i){if(!i){return}var h=this;i.$el.fadeOut(h.fxSpeed,function(){i.off();i.remove();delete h.hdaViews[i.model.id];if(_.isEmpty(h.hdaViews)){h.$el.find(h.emptyMsgSelector).fadeIn(h.fxSpeed,function(){h.trigger("empty-history",h)})}})},renderHdas:function(j){j=j||this.$el;this.hdaViews={};var i=this,h=j.find(this.datasetsSelector),k=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);h.empty();if(k.length){k.each(function(l){h.prepend(i.createHdaView(l).$el)});j.find(this.emptyMsgSelector).hide()}else{j.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(){var h=arguments;_.each(this.hdaViews,function(i){if(i.tagsEditor){i.tagsEditor.toggle.apply(i.tagsEditor,h)}})},toggleHDAAnnotationEditors:function(h){var i=arguments;_.each(this.hdaViews,function(j){if(j.annotationEditor){j.annotationEditor.toggle.apply(j.annotationEditor,i)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(h){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(h){h.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(i){var j=this;function l(m){j.searchFor=m;j.filters=[function(n){return n.matchesAll(j.searchFor)}];j.trigger("search:searching",m,j);j.renderHdas()}function h(m){if(j.model.hdas.haveDetails()){l(m);return}j.$el.find(".history-search-controls").searchInput("toggle-loading");j.model.hdas.fetchAllDetails({silent:true}).always(function(){j.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){l(m)})}function k(){j.searchFor="";j.filters=[];j.trigger("search:clear",j);j.renderHdas()}return i.searchInput({initialVal:j.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:h,onsearch:l,onclear:k})},toggleSearchControls:function(){var h=this.$el.find(".history-search-controls");if(!h.children().size()){h=this.renderSearchControls(h).hide()}h.slideToggle(this.fxSpeed,function(){if($(this).is(":visible")){this.searching=true;$(this).find("input").focus()}else{this.searching=false}})},showSelectors:function(h){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(h);_.each(this.hdaViews,function(i){i.showSelector(h)})},hideSelectors:function(h){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(h);_.each(this.hdaViews,function(i){i.hideSelector(h)})},toggleSelectors:function(h){if(!this.selecting){this.showSelectors(h)}else{this.hideSelectors(h)}},selectAllDatasets:function(i){var h=this.$el.find(".history-select-all-datasets-btn");currMode=h.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(j){j.select(i)});h.data("mode","deselect");h.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(j){j.deselect(i)});h.data("mode","select");h.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(h){return h.selected})},getSelectedHdaCollection:function(){return new d.HDACollection(_.map(this.getSelectedHdaViews(),function(h){return h.model}),{historyId:this.model.id})},showLoadingIndicator:function(i,h,j){h=(h!==undefined)?(h):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,j)}else{this.$el.fadeOut(h);this.indicator.show(i,h,j)}},hideLoadingIndicator:function(h,i){h=(h!==undefined)?(h):(this.fxSpeed);if(this.indicator){this.indicator.hide(h,i)}},displayMessage:function(m,n,l){var j=this;this.scrollToTop();var k=this.$el.find(this.msgsSelector),h=$("<div/>").addClass(m+"message").html(n);if(!_.isEmpty(l)){var i=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(j.messageToModalOptions(m,n,l));return false});h.append(" ",i)}return k.html(h)},messageToModalOptions:function(l,n,k){var h=this,m=$("<div/>"),j={title:"Details"};function i(o){o=_.omit(o,_.functions(o));return["<table>",_.map(o,function(q,p){q=(_.isObject(q))?(i(q)):(q);return'<tr><td style="vertical-align: top; color: grey">'+p+'</td><td style="padding-left: 8px">'+q+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(k)){j.body=m.append(i(k))}else{j.body=m.html(k)}j.buttons={Ok:function(){Galaxy.modal.hide();h.clearMessages()}};return j},clearMessages:function(){var h=this.$el.find(this.msgsSelector);h.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(h){this.$el.parent().scrollTop(h)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(i,j){if(!j){this.$el.parent().parent().scrollTop(i);return this}var h=window,k=this.$el.parent().parent(),m=$(h).innerHeight(),l=(m/2)-(j/2);$(k).scrollTop(i-l);return this},scrollToId:function(i){if((!i)||(!this.hdaViews[i])){return this}var h=this.hdaViews[i].$el;this.scrollIntoView(h.offset().top,h.outerHeight());return this},scrollToHid:function(h){var i=this.model.hdas.getByHid(h);if(!i){return this}return this.scrollToId(i.id)},connectToQuotaMeter:function(h){if(!h){return this}this.listenTo(h,"quota:over",this.showQuotaMessage);this.listenTo(h,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(h&&h.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var h=this.$el.find(".quota-message");if(h.is(":hidden")){h.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var h=this.$el.find(".quota-message");if(!h.is(":hidden")){h.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(h){if(!h){return this}this.on("new-storage",function(j,i){if(h&&j){h.findItemByHtml(_l("Include Deleted Datasets")).checked=j.get("show_deleted");h.findItemByHtml(_l("Include Hidden Datasets")).checked=j.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){j.find(".history-name").text(l);k.model.save({name:l}).fail(function(){j.find(".history-name").text(k.model.previous("name"))})}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(k){var l=this;function n(o){l.searchFor=o;l.filters=[function(p){return p.matchesAll(l.searchFor)}];l.trigger("search:searching",o,l);l.renderHdas()}function j(o){if(l.model.hdas.haveDetails()){n(o);return}l.$el.find(".history-search-controls").searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){n(o)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}return k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m})},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls");if(!k.children().size()){k=this.renderSearchControls(k).hide()}k.show(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").hide(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ 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: dan: When setting external metadata using _handle_metadata_externally (e.g. local and lwr runners) use the requirments of the set metadata tool to determine dependencies. Resolves issue seen with missing samtools command when samtools is not in the path, but has been installed with the dependency system.
by commits-noreply＠bitbucket.org 12 Dec '13

12 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4241eff3f67c/ Changeset: 4241eff3f67c User: dan Date: 2013-12-12 23:09:29 Summary: When setting external metadata using _handle_metadata_externally (e.g. local and lwr runners) use the requirments of the set metadata tool to determine dependencies. Resolves issue seen with missing samtools command when samtools is not in the path, but has been installed with the dependency system. Affected #: 4 files diff -r db9256a668eb13072231de605ca74e6c9372a467 -r 4241eff3f67c3d42fe51564c52aafabf65cc6130 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -598,6 +598,9 @@ tool_xml_text = """ <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata"><type class="SetMetadataTool" module="galaxy.tools"/> + <requirements> + <requirement type="package">samtools</requirement> + </requirements><action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/><command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command><inputs> diff -r db9256a668eb13072231de605ca74e6c9372a467 -r 4241eff3f67c3d42fe51564c52aafabf65cc6130 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -198,7 +198,7 @@ log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) return output_pairs - def _handle_metadata_externally(self, job_wrapper): + def _handle_metadata_externally( self, job_wrapper, resolve_requirements=False ): """ Set metadata externally. Used by the local and lwr job runners where this shouldn't be attached to command-line to execute. @@ -213,6 +213,12 @@ #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior kwds={ 'overwrite' : False } ) log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) + if resolve_requirements: + dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() + if dependency_shell_commands: + if isinstance( dependency_shell_commands, list ): + dependency_shell_commands = "&&".join( dependency_shell_commands ) + external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) external_metadata_proc = subprocess.Popen( args=external_metadata_script, shell=True, env=os.environ, diff -r db9256a668eb13072231de605ca74e6c9372a467 -r 4241eff3f67c3d42fe51564c52aafabf65cc6130 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -110,7 +110,7 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - self._handle_metadata_externally( job_wrapper ) + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job! try: job_wrapper.finish( stdout, stderr, exit_code ) diff -r db9256a668eb13072231de605ca74e6c9372a467 -r 4241eff3f67c3d42fe51564c52aafabf65cc6130 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -204,7 +204,7 @@ log.exception("failure running job %d" % job_wrapper.job_id) return if not LwrJobRunner.__remote_metadata( client ): - self._handle_metadata_externally( job_wrapper ) + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job try: job_wrapper.finish( stdout, stderr ) 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: carlfeberhard: History options menu: fix 'collapse expanded datasets' when no event
by commits-noreply＠bitbucket.org 12 Dec '13

12 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db9256a668eb/ Changeset: db9256a668eb User: carlfeberhard Date: 2013-12-12 22:55:48 Summary: History options menu: fix 'collapse expanded datasets' when no event Affected #: 2 files diff -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 -r db9256a668eb13072231de605ca74e6c9372a467 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -423,7 +423,7 @@ toggleBodyVisibility : function( event, expand ){ // bail (with propagation) if keydown and not space or enter var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; - if( ( event.type === 'keydown' ) + if( event && ( event.type === 'keydown' ) && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ return true; } diff -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 -r db9256a668eb13072231de605ca74e6c9372a467 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if((f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView: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: carlfeberhard: History panel: when clicking either annotation or tag button in history (top) open/close annotation or tag displays in history's hdas as well
by commits-noreply＠bitbucket.org 12 Dec '13

12 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bfccf1f3269e/ Changeset: bfccf1f3269e User: carlfeberhard Date: 2013-12-12 21:21:15 Summary: History panel: when clicking either annotation or tag button in history (top) open/close annotation or tag displays in history's hdas as well Affected #: 9 files diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -173,6 +173,7 @@ //============================================================================== var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */{ +//TODO: since this is a mixin, consider moving toggle, hidden into HUAVOptions /** */ hiddenUntilActivated : function( $activator, options ){ @@ -184,7 +185,9 @@ showSpeed : 'fast' }; _.extend( this.HUAVOptions, options || {}); + /** has this been shown already (and onshowFirstTime called)? */ this.HUAVOptions.hasBeenShown = this.HUAVOptions.$elementShown.is( ':visible' ); + this.hidden = this.isHidden(); if( $activator ){ var mixin = this; @@ -194,22 +197,34 @@ } }, + isHidden : function(){ + return ( this.HUAVOptions.$elementShown.is( ':hidden' ) ); + }, + /** */ toggle : function(){ // can be called manually as well with normal toggle arguments - if( this.HUAVOptions.$elementShown.is( ':hidden' ) ){ + if( this.isHidden() ){ // fire the optional fns on the first/each showing - good for render() if( !this.HUAVOptions.hasBeenShown ){ if( _.isFunction( this.HUAVOptions.onshowFirstTime ) ){ this.HUAVOptions.hasBeenShown = true; this.HUAVOptions.onshowFirstTime.call( this ); } - } else { - if( _.isFunction( this.HUAVOptions.onshow ) ){ - this.HUAVOptions.onshow.call( this ); - } } + if( _.isFunction( this.HUAVOptions.onshow ) ){ + this.HUAVOptions.onshow.call( this ); + } + this.hidden = false; + + } else { + if( _.isFunction( this.HUAVOptions.onhide ) ){ + this.HUAVOptions.onhide.call( this ); + } + this.hidden = true; } + //TODO: better as a callback (when the show/hide is actually done) + this.trigger( 'hiddenUntilActivated:' + (( this.isHidden() )?( 'shown' ):( 'hidden' )), this ); return this.HUAVOptions.showFn.apply( this.HUAVOptions.$elementShown, arguments ); } }; diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -46,11 +46,11 @@ /** is the view currently in selection mode? */ this.selectable = attributes.selectable || false; /** is the view currently selected? */ - this.selected = attributes.selected || false; - /** is the body of this hda view expanded/not. */ - this.expanded = attributes.expanded || false; - /** is the body of this hda view expanded/not. */ - this.draggable = attributes.draggable || false; + this.selected = attributes.selected || false; + /** is the body of this hda view expanded/not? */ + this.expanded = attributes.expanded || false; + /** is the body of this hda view expanded/not? */ + this.draggable = attributes.draggable || false; this._setUpListeners(); }, diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -33,6 +33,11 @@ this._render_rerunButton ]; + //TODO: move to HiddenUntilActivatedViewMixin + /** should the tags editor be shown or hidden initially? */ + this.tagsEditorShown = attributes.tagsEditorShown || false; + /** should the tags editor be shown or hidden initially? */ + this.annotationEditorShown = attributes.annotationEditorShown || false; }, // ......................................................................... edit attr, delete @@ -298,6 +303,7 @@ // more actions/buttons if( this.hasUser ){ $body.find( '.dataset-actions .left' ).append( this._render_visualizationsButton() ); + //TODO: might be better to move these into the render() and call setElement here this._renderTags( $body ); this._renderAnnotation( $body ); } @@ -305,28 +311,38 @@ }, _renderTags : function( $where ){ + var view = this; this.tagsEditor = new TagsEditor({ model : this.model, el : $where.find( '.tags-display' ), onshowFirstTime : function(){ this.render(); }, + // persist state on the hda view (and not the editor) since these are currently re-created each time + onshow : function(){ view.tagsEditorShown = true; }, + onhide : function(){ view.tagsEditorShown = false; }, $activator : faIconButton({ title : _l( 'Edit dataset tags' ), classes : 'dataset-tag-btn', faIcon : 'fa-tags' }).appendTo( $where.find( '.dataset-actions .right' ) ) }); + if( this.tagsEditorShown ){ this.tagsEditor.toggle( true ); } }, _renderAnnotation : function( $where ){ + var view = this; this.annotationEditor = new AnnotationEditor({ model : this.model, el : $where.find( '.annotation-display' ), onshowFirstTime : function(){ this.render(); }, + // persist state on the hda view (and not the editor) since these are currently re-created each time + onshow : function(){ view.annotationEditorShown = true; }, + onhide : function(){ view.annotationEditorShown = false; }, $activator : faIconButton({ title : _l( 'Edit dataset annotation' ), classes : 'dataset-annotate-btn', faIcon : 'fa-comment' }).appendTo( $where.find( '.dataset-actions .right' ) ) }); + if( this.annotationEditorShown ){ this.annotationEditor.toggle( true ); } }, makeDbkeyEditLink : function( $body ){ diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -116,11 +116,27 @@ // ........................................................................ common queries /** is this model already associated with a user? */ +//TODO: remove hasUser : function(){ var user = this.get( 'user' ); return !!( user && user.id ); }, + /** T/F is this history owned by the current user (Galaxy.currUser) + * Note: that this will return false for an anon user even if the history is theirs. + */ + ownedByCurrUser : function(){ + // no currUser + if( !Galaxy || !Galaxy.currUser ){ + return false; + } + // user is anon or history isn't owned + if( Galaxy.currUser.isAnonymous() || Galaxy.currUser.id !== this.get( 'user_id' ) ){ + return false; + } + return true; + }, + hdaCount : function(){ return _.reduce( _.values( this.get( 'state_details' ) ), function( memo, num ){ return memo + num; }, 0 ); }, diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -109,6 +109,7 @@ this.log( this + '.initialize:', attributes ); // ---- set up instance vars + /** which backbone view class to use when displaying the hda list */ this.HDAViewClass = attributes.HDAViewClass || this.defaultHDAViewClass; /** where should pages from links be displayed? (default to new tab/window) */ this.linkTarget = attributes.linkTarget || '_blank'; @@ -127,6 +128,11 @@ /** is the panel currently showing the dataset selection controls? */ this.selecting = attributes.selecting || false; + /** should the tags editor be shown or hidden initially? */ + this.tagsEditorShown = attributes.tagsShown || false; + /** should the tags editor be shown or hidden initially? */ + this.annotationEditorShown = attributes.annotationEditorShown || false; + this._setUpListeners(); // ---- handle models passed on init @@ -576,10 +582,20 @@ }, _renderTags : function( $where ){ + var panel = this; this.tagsEditor = new TagsEditor({ model : this.model, el : $where.find( '.history-controls .tags-display' ), onshowFirstTime : function(){ this.render(); }, + // show hide hda view tag editors when this is shown/hidden + onshow : function(){ + panel.tagsEditorShown = true; + panel.toggleHDATagEditors( true, panel.fxSpeed ); + }, + onhide : function(){ + panel.tagsEditorShown = false; + panel.toggleHDATagEditors( false, panel.fxSpeed ); + }, $activator : faIconButton({ title : _l( 'Edit history tags' ), classes : 'history-tag-btn', @@ -588,12 +604,22 @@ }); }, _renderAnnotation : function( $where ){ + var panel = this; this.annotationEditor = new AnnotationEditor({ model : this.model, el : $where.find( '.history-controls .annotation-display' ), onshowFirstTime : function(){ this.render(); }, + // show hide hda view annotation editors when this is shown/hidden + onshow : function(){ + panel.annotationEditorShown = true; + panel.toggleHDAAnnotationEditors( true, panel.fxSpeed ); + }, + onhide : function(){ + panel.annotationEditorShown = false; + panel.toggleHDAAnnotationEditors( false, panel.fxSpeed ); + }, $activator : faIconButton({ - title : _l( 'Edit history tags' ), + title : _l( 'Edit history Annotation' ), classes : 'history-annotate-btn', faIcon : 'fa-comment' }).appendTo( $where.find( '.history-secondary-actions' ) ) @@ -733,8 +759,10 @@ linkTarget : this.linkTarget, expanded : expanded, //draggable : true, + tagsEditorShown : this.tagsEditorShown, + annotationEditorShown : this.annotationEditorShown, selectable : this.selecting, - hasUser : this.model.hasUser(), + hasUser : this.model.ownedByCurrUser(), logger : this.logger }); this._setUpHdaListeners( hdaView ); @@ -832,6 +860,26 @@ return this.hdaViews; }, + /** toggle the visibility of each hdaView's tagsEditor applying all the args sent to this function */ + toggleHDATagEditors : function(){ + var args = arguments; + _.each( this.hdaViews, function( hdaView ){ + if( hdaView.tagsEditor ){ + hdaView.tagsEditor.toggle.apply( hdaView.tagsEditor, args ); + } + }); + }, + + /** toggle the visibility of each hdaView's annotationEditor applying all the args sent to this function */ + toggleHDAAnnotationEditors : function( showOrHide ){ + var args = arguments; + _.each( this.hdaViews, function( hdaView ){ + if( hdaView.annotationEditor ){ + hdaView.annotationEditor.toggle.apply( hdaView.annotationEditor, args ); + } + }); + }, + // ------------------------------------------------------------------------ panel events /** event map */ events : { diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},toggle:function(){if(this.HUAVOptions.$elementShown.is(":hidden")){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}else{if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}}}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.isHidden()){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this)}this.hidden=true}this.trigger("hiddenUntilActivated:"+((this.isHidden())?("shown"):("hidden")),this);return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="'+this.linkTarget+'">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="'+this.linkTarget+'">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(a){var c=Backbone.Model.extend(LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",renameUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"history/rename_async?id="+this.get("id")},annotateUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"history/annotate_async?id="+this.get("id")},tagUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(f,g,e){e=e||{};this.logger=e.logger||null;this.log(this+".initialize:",f,g,e);this.hdas=new a.HDACollection(g||[],{historyId:this.get("id")});if(g&&_.isArray(g)){this.hdas.reset(g)}this._setUpListeners();this.updateTimeoutId=null;this.checkForUpdates()},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(f,e){if(this.hdas){this.hdas.historyId=e}},this)},errorHandler:function(f,i,e,h,g){this.clearUpdateTimeout()},hasUser:function(){var e=this.get("user");return !!(e&&e.id)},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(e,f){return e+f},0)},checkForUpdates:function(e){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(e)){e.call(this)}}return this},setUpdateTimeout:function(e){e=e||c.UPDATE_DELAY;var f=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){f.refresh()},e);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(f,e){f=f||[];e=e||{};var g=this;e.data=e.data||{};if(f.length){e.data.details=f.join(",")}var h=this.hdas.fetch(e);h.done(function(i){g.checkForUpdates(function(){this.fetch()})});return h},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});c.UPDATE_DELAY=4000;c.getHistoryData=function d(f,p){p=p||{};var j=p.hdaDetailIds||[];var l=jQuery.Deferred(),k=null;function g(q){return jQuery.ajax(galaxy_config.root+"api/histories/"+f)}function e(q){if(!q||!q.state_ids){return 0}return _.reduce(q.state_ids,function(r,t,s){return r+t.length},0)}function o(r){if(!e(r)){return[]}if(_.isFunction(j)){j=j(r)}var q=(j.length)?({details:j.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+r.id+"/contents",{data:q})}var n=p.historyFn||g,m=p.hdaFn||o;var i=n(f);i.done(function(q){k=q;l.notify({status:"history data retrieved",historyJSON:k})});i.fail(function(s,q,r){l.reject(s,"loading the history")});var h=i.then(m);h.then(function(q){l.notify({status:"dataset data retrieved",historyJSON:k,hdaJSON:q});l.resolve(k,q)});h.fail(function(s,q,r){l.reject(s,"loading the datasets",{history:k})});return l};var b=Backbone.Collection.extend(LoggableMixin).extend({model:c,urlRoot:galaxy_config.root+"api/histories"});return{History:c,HistoryCollection:b}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(a){var c=Backbone.Model.extend(LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",renameUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"history/rename_async?id="+this.get("id")},annotateUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"history/annotate_async?id="+this.get("id")},tagUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(f,g,e){e=e||{};this.logger=e.logger||null;this.log(this+".initialize:",f,g,e);this.hdas=new a.HDACollection(g||[],{historyId:this.get("id")});if(g&&_.isArray(g)){this.hdas.reset(g)}this._setUpListeners();this.updateTimeoutId=null;this.checkForUpdates()},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(f,e){if(this.hdas){this.hdas.historyId=e}},this)},errorHandler:function(f,i,e,h,g){this.clearUpdateTimeout()},hasUser:function(){var e=this.get("user");return !!(e&&e.id)},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(e,f){return e+f},0)},checkForUpdates:function(e){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(e)){e.call(this)}}return this},setUpdateTimeout:function(e){e=e||c.UPDATE_DELAY;var f=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){f.refresh()},e);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(f,e){f=f||[];e=e||{};var g=this;e.data=e.data||{};if(f.length){e.data.details=f.join(",")}var h=this.hdas.fetch(e);h.done(function(i){g.checkForUpdates(function(){this.fetch()})});return h},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});c.UPDATE_DELAY=4000;c.getHistoryData=function d(f,p){p=p||{};var j=p.hdaDetailIds||[];var l=jQuery.Deferred(),k=null;function g(q){return jQuery.ajax(galaxy_config.root+"api/histories/"+f)}function e(q){if(!q||!q.state_ids){return 0}return _.reduce(q.state_ids,function(r,t,s){return r+t.length},0)}function o(r){if(!e(r)){return[]}if(_.isFunction(j)){j=j(r)}var q=(j.length)?({details:j.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+r.id+"/contents",{data:q})}var n=p.historyFn||g,m=p.hdaFn||o;var i=n(f);i.done(function(q){k=q;l.notify({status:"history data retrieved",historyJSON:k})});i.fail(function(s,q,r){l.reject(s,"loading the history")});var h=i.then(m);h.then(function(q){l.notify({status:"dataset data retrieved",historyJSON:k,hdaJSON:q});l.resolve(k,q)});h.fail(function(s,q,r){l.reject(s,"loading the datasets",{history:k})});return l};var b=Backbone.Collection.extend(LoggableMixin).extend({model:c,urlRoot:galaxy_config.root+"api/histories"});return{History:c,HistoryCollection:b}}); \ No newline at end of file diff -r 8946e734862f662715142fb333f385caa0dda6ea -r bfccf1f3269e0f71d2a07a0dda9b6c64734f1c58 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(g,d,b,a){var c=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(h){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([h],[true])))},removeExpandedHda:function(h){this.save("expandedHdas",_.omit(this.get("expandedHdas"),h))},toString:function(){return"HistoryPanelPrefs("+this.id+")"}});c.historyStorageKey=function f(h){if(!h){throw new Error("HistoryPanelPrefs.historyStorageKey needs valid id: "+h)}return("history:"+h)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(h){h=h||{};if(h.logger){this.logger=h.logger}this.log(this+".initialize:",h);this.HDAViewClass=h.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=h.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];this.searching=h.searching||false;this.selecting=h.selecting||false;this._setUpListeners();if(this.model){this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers()}if(h.onready){h.onready.call(this)}},_setUpListeners:function(){this.on("error",function(i,l,h,k,j){this.errorHandler(i,l,h,k,j)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(h){this.log(this+"",arguments)},this)}},errorHandler:function(j,m,i,l,k){var h=this._parseErrorMessage(j,m,i,l,k);if(m&&m.status===0&&m.readyState===0){}else{if(m&&m.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",h.message,h.details)})}else{this.displayMessage("error",h.message,h.details)}}}},_parseErrorMessage:function(k,o,j,n,m){var i=Galaxy.currUser,h={message:this._bePolite(n),details:{user:(i instanceof User)?(i.toJSON()):(i+""),source:(k instanceof Backbone.Model)?(k.toJSON()):(k+""),xhr:o,options:(o)?(_.omit(j,"xhr")):(j)}};_.extend(h.details,m||{});if(o&&_.isFunction(o.getAllResponseHeaders)){var l=o.getAllResponseHeaders();l=_.compact(l.split("\n"));l=_.map(l,function(p){return p.split(": ")});h.details.xhr.responseHeaders=_.object(l)}return h},_bePolite:function(h){h=h||_l("An error occurred while getting updates from the server");return h+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(i){var h=this;return this.loadHistoryWithHDADetails("current",i).then(function(k,j){h.trigger("current-history",h)})},switchToHistory:function(k,j){var h=this,i=function(){return jQuery.post(galaxy_config.root+"api/histories/"+k+"/set_as_current")};return this.loadHistoryWithHDADetails(k,j,i).then(function(m,l){h.trigger("switched-history",h)})},createNewHistory:function(j){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var h=this,i=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,j,i).then(function(l,k){h.trigger("new-history",h)})},loadHistoryWithHDADetails:function(k,j,i,m){var h=this,l=function(n){return h.getExpandedHdaIds(n.id)};return this.loadHistory(k,j,i,m,l)},loadHistory:function(k,j,i,n,l){this.trigger("loading-history",this);j=j||{};var h=this;var m=g.History.getHistoryData(k,{historyFn:i,hdaFn:n,hdaDetailIds:j.initiallyExpanded||l});return this._loadHistoryFromXHR(m,j).fail(function(q,o,p){h.trigger("error",h,q,j,_l("An error was encountered while "+o),{historyId:k,history:p||{}})}).always(function(){h.trigger("loading-done",h)})},_loadHistoryFromXHR:function(j,i){var h=this;j.then(function(k,l){h.setModel(k,l,i)});j.fail(function(l,k){h.render()});return j},setModel:function(j,h,i){i=i||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){j.user=Galaxy.currUser.toJSON()}this.model=new g.History(j,h,i);this._setUpWebStorage(i.initiallyExpanded,i.show_deleted,i.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(i,h,j){this.storage=new c({id:c.historyStorageKey(this.model.get("id"))});if(_.isObject(i)){this.storage.set("exandedHdas",i)}if(_.isBoolean(h)){this.storage.set("show_deleted",h)}if(_.isBoolean(j)){this.storage.set("show_hidden",j)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var h in sessionStorage){if(h.indexOf("history:")===0){sessionStorage.removeItem(h)}}},getStoredOptions:function(i){if(!i||i==="current"){return(this.storage)?(this.storage.get()):({})}var h=sessionStorage.getItem(c.historyStorageKey(i));return(h===null)?({}):(JSON.parse(h))},getExpandedHdaIds:function(h){var i=this.getStoredOptions(h).expandedHdas;return((_.isEmpty(i))?([]):(_.keys(i)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(i,k,h,j){this.errorHandler(i,k,h,j)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(h){this.model.fetch()},this);this.model.hdas.on("state:ready",function(i,j,h){if((!i.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[i.id])}},this)},render:function(j,k){j=(j===undefined)?(this.fxSpeed):(j);var h=this,i;if(this.model){i=this.renderModel()}else{i=this.renderWithoutModel()}$(h).queue("fx",[function(l){if(j&&h.$el.is(":visible")){h.$el.fadeOut(j,l)}else{l()}},function(l){h.$el.empty();if(i){h.$el.append(i.children())}l()},function(l){if(j&&!h.$el.is(":visible")){h.$el.fadeIn(j,l)}else{l()}},function(l){if(k){k.call(this)}h.trigger("rendered",this);l()}]);return this},renderWithoutModel:function(){var h=$("<div/>"),i=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return h.append(i)},renderModel:function(){var h=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){h.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{h.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(h);this._renderAnnotation(h)}}h.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(h);this.renderHdas(h);return h},_renderTags:function(h){this.tagsEditor=new TagsEditor({model:this.model,el:h.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".history-secondary-actions"))})},_renderAnnotation:function(h){this.annotationEditor=new AnnotationEditor({model:this.model,el:h.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".history-secondary-actions"))})},_renderSearchButton:function(h){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(h){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(h){h=h||this.$el;h.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var i=this;h.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(j){h.find(".history-name").text(j);i.model.save({name:j}).fail(function(){h.find(".history-name").text(i.model.previous("name"))})}});this._setUpDatasetActionsPopup(h)},_setUpDatasetActionsPopup:function(h){var i=this;(new PopupMenu(h.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.hide;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Unhide datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.unhide;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Delete datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype["delete"];i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Undelete datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.undelete;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var j=d.HistoryDatasetAssociation.prototype.purge;i.getSelectedHdaCollection().ajaxQueue(j)}}}]))},refreshHdas:function(i,h){if(this.model){return this.model.refresh(i,h)}return $.when()},addHdaView:function(k){this.log("add."+this,k);var i=this;if(!k.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function j(m){var l=i.$el.find(i.emptyMsgSelector);if(l.is(":visible")){l.fadeOut(i.fxSpeed,m)}else{m()}},function h(m){i.scrollToTop();var l=i.$el.find(i.datasetsSelector);i.createHdaView(k).$el.hide().prependTo(l).slideDown(i.fxSpeed)}])},createHdaView:function(j){var i=j.get("id"),h=this.storage.get("expandedHdas")[i],k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:h,selectable:this.selecting,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(k);this.hdaViews[i]=k;return k.render()},_setUpHdaListeners:function(i){var h=this;i.on("body-expanded",function(j){h.storage.addExpandedHda(j)});i.on("body-collapsed",function(j){h.storage.removeExpandedHda(j)});i.on("error",function(k,m,j,l){h.errorHandler(k,m,j,l)})},handleHdaDeletionChange:function(h){if(h.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[h.id])}},handleHdaVisibleChange:function(h){if(h.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[h.id])}},removeHdaView:function(i){if(!i){return}var h=this;i.$el.fadeOut(h.fxSpeed,function(){i.off();i.remove();delete h.hdaViews[i.model.id];if(_.isEmpty(h.hdaViews)){h.$el.find(h.emptyMsgSelector).fadeIn(h.fxSpeed,function(){h.trigger("empty-history",h)})}})},renderHdas:function(j){j=j||this.$el;this.hdaViews={};var i=this,h=j.find(this.datasetsSelector),k=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);h.empty();if(k.length){k.each(function(l){h.prepend(i.createHdaView(l).$el)});j.find(this.emptyMsgSelector).hide()}else{j.find(this.emptyMsgSelector).show()}return this.hdaViews},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(h){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(h){h.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(i){var j=this;function l(m){j.searchFor=m;j.filters=[function(n){return n.matchesAll(j.searchFor)}];j.trigger("search:searching",m,j);j.renderHdas()}function h(m){if(j.model.hdas.haveDetails()){l(m);return}j.$el.find(".history-search-controls").searchInput("toggle-loading");j.model.hdas.fetchAllDetails({silent:true}).always(function(){j.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){l(m)})}function k(){j.searchFor="";j.filters=[];j.trigger("search:clear",j);j.renderHdas()}return i.searchInput({initialVal:j.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:h,onsearch:l,onclear:k})},toggleSearchControls:function(){var h=this.$el.find(".history-search-controls");if(!h.children().size()){h=this.renderSearchControls(h).hide()}h.slideToggle(this.fxSpeed,function(){if($(this).is(":visible")){this.searching=true;$(this).find("input").focus()}else{this.searching=false}})},showSelectors:function(h){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(h);_.each(this.hdaViews,function(i){i.showSelector(h)})},hideSelectors:function(h){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(h);_.each(this.hdaViews,function(i){i.hideSelector(h)})},toggleSelectors:function(h){if(!this.selecting){this.showSelectors(h)}else{this.hideSelectors(h)}},selectAllDatasets:function(i){var h=this.$el.find(".history-select-all-datasets-btn");currMode=h.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(j){j.select(i)});h.data("mode","deselect");h.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(j){j.deselect(i)});h.data("mode","select");h.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(h){return h.selected})},getSelectedHdaCollection:function(){return new d.HDACollection(_.map(this.getSelectedHdaViews(),function(h){return h.model}),{historyId:this.model.id})},showLoadingIndicator:function(i,h,j){h=(h!==undefined)?(h):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,j)}else{this.$el.fadeOut(h);this.indicator.show(i,h,j)}},hideLoadingIndicator:function(h,i){h=(h!==undefined)?(h):(this.fxSpeed);if(this.indicator){this.indicator.hide(h,i)}},displayMessage:function(m,n,l){var j=this;this.scrollToTop();var k=this.$el.find(this.msgsSelector),h=$("<div/>").addClass(m+"message").html(n);if(!_.isEmpty(l)){var i=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(j.messageToModalOptions(m,n,l));return false});h.append(" ",i)}return k.html(h)},messageToModalOptions:function(l,n,k){var h=this,m=$("<div/>"),j={title:"Details"};function i(o){o=_.omit(o,_.functions(o));return["<table>",_.map(o,function(q,p){q=(_.isObject(q))?(i(q)):(q);return'<tr><td style="vertical-align: top; color: grey">'+p+'</td><td style="padding-left: 8px">'+q+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(k)){j.body=m.append(i(k))}else{j.body=m.html(k)}j.buttons={Ok:function(){Galaxy.modal.hide();h.clearMessages()}};return j},clearMessages:function(){var h=this.$el.find(this.msgsSelector);h.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(h){this.$el.parent().scrollTop(h)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(i,j){if(!j){this.$el.parent().parent().scrollTop(i);return this}var h=window,k=this.$el.parent().parent(),m=$(h).innerHeight(),l=(m/2)-(j/2);$(k).scrollTop(i-l);return this},scrollToId:function(i){if((!i)||(!this.hdaViews[i])){return this}var h=this.hdaViews[i].$el;this.scrollIntoView(h.offset().top,h.outerHeight());return this},scrollToHid:function(h){var i=this.model.hdas.getByHid(h);if(!i){return this}return this.scrollToId(i.id)},connectToQuotaMeter:function(h){if(!h){return this}this.listenTo(h,"quota:over",this.showQuotaMessage);this.listenTo(h,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(h&&h.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var h=this.$el.find(".quota-message");if(h.is(":hidden")){h.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var h=this.$el.find(".quota-message");if(!h.is(":hidden")){h.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(h){if(!h){return this}this.on("new-storage",function(j,i){if(h&&j){h.findItemByHtml(_l("Include Deleted Datasets")).checked=j.get("show_deleted");h.findItemByHtml(_l("Include Hidden Datasets")).checked=j.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(g,d,b,a){var c=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(h){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([h],[true])))},removeExpandedHda:function(h){this.save("expandedHdas",_.omit(this.get("expandedHdas"),h))},toString:function(){return"HistoryPanelPrefs("+this.id+")"}});c.historyStorageKey=function f(h){if(!h){throw new Error("HistoryPanelPrefs.historyStorageKey needs valid id: "+h)}return("history:"+h)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(h){h=h||{};if(h.logger){this.logger=h.logger}this.log(this+".initialize:",h);this.HDAViewClass=h.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=h.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];this.searching=h.searching||false;this.selecting=h.selecting||false;this.tagsEditorShown=h.tagsShown||false;this.annotationEditorShown=h.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers()}if(h.onready){h.onready.call(this)}},_setUpListeners:function(){this.on("error",function(i,l,h,k,j){this.errorHandler(i,l,h,k,j)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(h){this.log(this+"",arguments)},this)}},errorHandler:function(j,m,i,l,k){var h=this._parseErrorMessage(j,m,i,l,k);if(m&&m.status===0&&m.readyState===0){}else{if(m&&m.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",h.message,h.details)})}else{this.displayMessage("error",h.message,h.details)}}}},_parseErrorMessage:function(k,o,j,n,m){var i=Galaxy.currUser,h={message:this._bePolite(n),details:{user:(i instanceof User)?(i.toJSON()):(i+""),source:(k instanceof Backbone.Model)?(k.toJSON()):(k+""),xhr:o,options:(o)?(_.omit(j,"xhr")):(j)}};_.extend(h.details,m||{});if(o&&_.isFunction(o.getAllResponseHeaders)){var l=o.getAllResponseHeaders();l=_.compact(l.split("\n"));l=_.map(l,function(p){return p.split(": ")});h.details.xhr.responseHeaders=_.object(l)}return h},_bePolite:function(h){h=h||_l("An error occurred while getting updates from the server");return h+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(i){var h=this;return this.loadHistoryWithHDADetails("current",i).then(function(k,j){h.trigger("current-history",h)})},switchToHistory:function(k,j){var h=this,i=function(){return jQuery.post(galaxy_config.root+"api/histories/"+k+"/set_as_current")};return this.loadHistoryWithHDADetails(k,j,i).then(function(m,l){h.trigger("switched-history",h)})},createNewHistory:function(j){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var h=this,i=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,j,i).then(function(l,k){h.trigger("new-history",h)})},loadHistoryWithHDADetails:function(k,j,i,m){var h=this,l=function(n){return h.getExpandedHdaIds(n.id)};return this.loadHistory(k,j,i,m,l)},loadHistory:function(k,j,i,n,l){this.trigger("loading-history",this);j=j||{};var h=this;var m=g.History.getHistoryData(k,{historyFn:i,hdaFn:n,hdaDetailIds:j.initiallyExpanded||l});return this._loadHistoryFromXHR(m,j).fail(function(q,o,p){h.trigger("error",h,q,j,_l("An error was encountered while "+o),{historyId:k,history:p||{}})}).always(function(){h.trigger("loading-done",h)})},_loadHistoryFromXHR:function(j,i){var h=this;j.then(function(k,l){h.setModel(k,l,i)});j.fail(function(l,k){h.render()});return j},setModel:function(j,h,i){i=i||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){j.user=Galaxy.currUser.toJSON()}this.model=new g.History(j,h,i);this._setUpWebStorage(i.initiallyExpanded,i.show_deleted,i.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(i,h,j){this.storage=new c({id:c.historyStorageKey(this.model.get("id"))});if(_.isObject(i)){this.storage.set("exandedHdas",i)}if(_.isBoolean(h)){this.storage.set("show_deleted",h)}if(_.isBoolean(j)){this.storage.set("show_hidden",j)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var h in sessionStorage){if(h.indexOf("history:")===0){sessionStorage.removeItem(h)}}},getStoredOptions:function(i){if(!i||i==="current"){return(this.storage)?(this.storage.get()):({})}var h=sessionStorage.getItem(c.historyStorageKey(i));return(h===null)?({}):(JSON.parse(h))},getExpandedHdaIds:function(h){var i=this.getStoredOptions(h).expandedHdas;return((_.isEmpty(i))?([]):(_.keys(i)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(i,k,h,j){this.errorHandler(i,k,h,j)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(h){this.model.fetch()},this);this.model.hdas.on("state:ready",function(i,j,h){if((!i.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[i.id])}},this)},render:function(j,k){j=(j===undefined)?(this.fxSpeed):(j);var h=this,i;if(this.model){i=this.renderModel()}else{i=this.renderWithoutModel()}$(h).queue("fx",[function(l){if(j&&h.$el.is(":visible")){h.$el.fadeOut(j,l)}else{l()}},function(l){h.$el.empty();if(i){h.$el.append(i.children())}l()},function(l){if(j&&!h.$el.is(":visible")){h.$el.fadeIn(j,l)}else{l()}},function(l){if(k){k.call(this)}h.trigger("rendered",this);l()}]);return this},renderWithoutModel:function(){var h=$("<div/>"),i=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return h.append(i)},renderModel:function(){var h=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){h.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{h.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(h);this._renderAnnotation(h)}}h.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(h);this.renderHdas(h);return h},_renderTags:function(h){var i=this;this.tagsEditor=new TagsEditor({model:this.model,el:h.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.tagsEditorShown=true;i.toggleHDATagEditors(true,i.fxSpeed)},onhide:function(){i.tagsEditorShown=false;i.toggleHDATagEditors(false,i.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".history-secondary-actions"))})},_renderAnnotation:function(h){var i=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:h.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.annotationEditorShown=true;i.toggleHDAAnnotationEditors(true,i.fxSpeed)},onhide:function(){i.annotationEditorShown=false;i.toggleHDAAnnotationEditors(false,i.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".history-secondary-actions"))})},_renderSearchButton:function(h){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(h){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(h){h=h||this.$el;h.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var i=this;h.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(j){h.find(".history-name").text(j);i.model.save({name:j}).fail(function(){h.find(".history-name").text(i.model.previous("name"))})}});this._setUpDatasetActionsPopup(h)},_setUpDatasetActionsPopup:function(h){var i=this;(new PopupMenu(h.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.hide;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Unhide datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.unhide;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Delete datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype["delete"];i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Undelete datasets"),func:function(){var j=d.HistoryDatasetAssociation.prototype.undelete;i.getSelectedHdaCollection().ajaxQueue(j)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var j=d.HistoryDatasetAssociation.prototype.purge;i.getSelectedHdaCollection().ajaxQueue(j)}}}]))},refreshHdas:function(i,h){if(this.model){return this.model.refresh(i,h)}return $.when()},addHdaView:function(k){this.log("add."+this,k);var i=this;if(!k.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function j(m){var l=i.$el.find(i.emptyMsgSelector);if(l.is(":visible")){l.fadeOut(i.fxSpeed,m)}else{m()}},function h(m){i.scrollToTop();var l=i.$el.find(i.datasetsSelector);i.createHdaView(k).$el.hide().prependTo(l).slideDown(i.fxSpeed)}])},createHdaView:function(j){var i=j.get("id"),h=this.storage.get("expandedHdas")[i],k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:h,tagsEditorShown:this.tagsEditorShown,annotationEditorShown:this.annotationEditorShown,selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(k);this.hdaViews[i]=k;return k.render()},_setUpHdaListeners:function(i){var h=this;i.on("body-expanded",function(j){h.storage.addExpandedHda(j)});i.on("body-collapsed",function(j){h.storage.removeExpandedHda(j)});i.on("error",function(k,m,j,l){h.errorHandler(k,m,j,l)})},handleHdaDeletionChange:function(h){if(h.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[h.id])}},handleHdaVisibleChange:function(h){if(h.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[h.id])}},removeHdaView:function(i){if(!i){return}var h=this;i.$el.fadeOut(h.fxSpeed,function(){i.off();i.remove();delete h.hdaViews[i.model.id];if(_.isEmpty(h.hdaViews)){h.$el.find(h.emptyMsgSelector).fadeIn(h.fxSpeed,function(){h.trigger("empty-history",h)})}})},renderHdas:function(j){j=j||this.$el;this.hdaViews={};var i=this,h=j.find(this.datasetsSelector),k=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);h.empty();if(k.length){k.each(function(l){h.prepend(i.createHdaView(l).$el)});j.find(this.emptyMsgSelector).hide()}else{j.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(){var h=arguments;_.each(this.hdaViews,function(i){if(i.tagsEditor){i.tagsEditor.toggle.apply(i.tagsEditor,h)}})},toggleHDAAnnotationEditors:function(h){var i=arguments;_.each(this.hdaViews,function(j){if(j.annotationEditor){j.annotationEditor.toggle.apply(j.annotationEditor,i)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(h){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(h){h.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(i){var j=this;function l(m){j.searchFor=m;j.filters=[function(n){return n.matchesAll(j.searchFor)}];j.trigger("search:searching",m,j);j.renderHdas()}function h(m){if(j.model.hdas.haveDetails()){l(m);return}j.$el.find(".history-search-controls").searchInput("toggle-loading");j.model.hdas.fetchAllDetails({silent:true}).always(function(){j.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){l(m)})}function k(){j.searchFor="";j.filters=[];j.trigger("search:clear",j);j.renderHdas()}return i.searchInput({initialVal:j.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:h,onsearch:l,onclear:k})},toggleSearchControls:function(){var h=this.$el.find(".history-search-controls");if(!h.children().size()){h=this.renderSearchControls(h).hide()}h.slideToggle(this.fxSpeed,function(){if($(this).is(":visible")){this.searching=true;$(this).find("input").focus()}else{this.searching=false}})},showSelectors:function(h){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(h);_.each(this.hdaViews,function(i){i.showSelector(h)})},hideSelectors:function(h){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(h);_.each(this.hdaViews,function(i){i.hideSelector(h)})},toggleSelectors:function(h){if(!this.selecting){this.showSelectors(h)}else{this.hideSelectors(h)}},selectAllDatasets:function(i){var h=this.$el.find(".history-select-all-datasets-btn");currMode=h.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(j){j.select(i)});h.data("mode","deselect");h.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(j){j.deselect(i)});h.data("mode","select");h.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(h){return h.selected})},getSelectedHdaCollection:function(){return new d.HDACollection(_.map(this.getSelectedHdaViews(),function(h){return h.model}),{historyId:this.model.id})},showLoadingIndicator:function(i,h,j){h=(h!==undefined)?(h):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,j)}else{this.$el.fadeOut(h);this.indicator.show(i,h,j)}},hideLoadingIndicator:function(h,i){h=(h!==undefined)?(h):(this.fxSpeed);if(this.indicator){this.indicator.hide(h,i)}},displayMessage:function(m,n,l){var j=this;this.scrollToTop();var k=this.$el.find(this.msgsSelector),h=$("<div/>").addClass(m+"message").html(n);if(!_.isEmpty(l)){var i=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(j.messageToModalOptions(m,n,l));return false});h.append(" ",i)}return k.html(h)},messageToModalOptions:function(l,n,k){var h=this,m=$("<div/>"),j={title:"Details"};function i(o){o=_.omit(o,_.functions(o));return["<table>",_.map(o,function(q,p){q=(_.isObject(q))?(i(q)):(q);return'<tr><td style="vertical-align: top; color: grey">'+p+'</td><td style="padding-left: 8px">'+q+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(k)){j.body=m.append(i(k))}else{j.body=m.html(k)}j.buttons={Ok:function(){Galaxy.modal.hide();h.clearMessages()}};return j},clearMessages:function(){var h=this.$el.find(this.msgsSelector);h.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(h){this.$el.parent().scrollTop(h)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(i,j){if(!j){this.$el.parent().parent().scrollTop(i);return this}var h=window,k=this.$el.parent().parent(),m=$(h).innerHeight(),l=(m/2)-(j/2);$(k).scrollTop(i-l);return this},scrollToId:function(i){if((!i)||(!this.hdaViews[i])){return this}var h=this.hdaViews[i].$el;this.scrollIntoView(h.offset().top,h.outerHeight());return this},scrollToHid:function(h){var i=this.model.hdas.getByHid(h);if(!i){return this}return this.scrollToId(i.id)},connectToQuotaMeter:function(h){if(!h){return this}this.listenTo(h,"quota:over",this.showQuotaMessage);this.listenTo(h,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(h&&h.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var h=this.$el.find(".quota-message");if(h.is(":hidden")){h.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var h=this.$el.find(".quota-message");if(!h.is(":hidden")){h.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(h){if(!h){return this}this.on("new-storage",function(j,i){if(h&&j){h.findItemByHtml(_l("Include Deleted Datasets")).checked=j.get("show_deleted");h.findItemByHtml(_l("Include Hidden Datasets")).checked=j.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ 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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