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https://github.com/galaxyproject/galaxy.git
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Automated merge.
This commit is contained in:
Jeremy Goecks
@@ -169,7 +169,7 @@ class AdminToolshed( AdminGalaxy ):
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message = kwd.get( 'message', '' )
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status = kwd.get( 'status', 'done' )
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tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
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if tool_dependency.in_error_state:
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message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). "
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message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems "
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@@ -806,7 +806,7 @@ class AdminToolshed( AdminGalaxy ):
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tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
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if tool_dependency_ids:
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# We need a tool_shed_repository, so get it from one of the tool_dependencies.
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tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
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tool_shed_repository = tool_dependency.tool_shed_repository
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else:
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# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
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@@ -830,7 +830,7 @@ class AdminToolshed( AdminGalaxy ):
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elif operation == 'uninstall':
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tool_dependencies_for_uninstallation = []
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for tool_dependency_id in tool_dependency_ids:
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tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
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if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.INSTALLED,
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trans.install_model.ToolDependency.installation_status.ERROR ]:
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tool_dependencies_for_uninstallation.append( tool_dependency )
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@@ -845,7 +845,7 @@ class AdminToolshed( AdminGalaxy ):
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if trans.app.config.tool_dependency_dir:
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tool_dependencies_for_installation = []
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for tool_dependency_id in tool_dependency_ids:
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tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
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if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
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trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
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tool_dependencies_for_installation.append( tool_dependency )
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@@ -889,7 +889,7 @@ class AdminToolshed( AdminGalaxy ):
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repository_id = kwd.get( 'repository_id', None )
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if tool_dependency_ids:
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# We need a tool_shed_repository, so get it from one of the tool_dependencies.
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tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
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tool_shed_repository = tool_dependency.tool_shed_repository
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else:
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# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
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@@ -914,7 +914,7 @@ class AdminToolshed( AdminGalaxy ):
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if trans.app.config.tool_dependency_dir:
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tool_dependencies_for_installation = []
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for tool_dependency_id in tool_dependency_ids:
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tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
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if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
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trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
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tool_dependencies_for_installation.append( tool_dependency )
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@@ -1849,7 +1849,7 @@ class AdminToolshed( AdminGalaxy ):
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tool_dependency_ids = util.listify( kwd.get( 'id', None ) )
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tool_dependencies = []
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for tool_dependency_id in tool_dependency_ids:
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tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
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tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
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tool_dependencies.append( tool_dependency )
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tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
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if kwd.get( 'uninstall_tool_dependencies_button', False ):
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@@ -1347,7 +1347,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
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match_tuples = []
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ok = True
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if tool_ids or tool_names or tool_versions:
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ok, match_tuples = search_util.search_repository_metadata( trans,
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ok, match_tuples = search_util.search_repository_metadata( trans.app,
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exact_matches_checked,
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tool_ids=tool_ids,
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tool_names=tool_names,
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@@ -1437,9 +1437,14 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
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match_tuples = []
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ok = True
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if workflow_names:
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ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names )
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ok, match_tuples = search_util.search_repository_metadata( trans.app,
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exact_matches_checked,
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workflow_names=workflow_names )
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else:
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ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True )
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ok, match_tuples = search_util.search_repository_metadata( trans.app,
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exact_matches_checked,
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workflow_names=[],
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all_workflows=True )
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if ok:
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kwd[ 'match_tuples' ] = match_tuples
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if trans.webapp.name == 'galaxy':
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@@ -81,15 +81,17 @@ def search_names_versions( tool_dict, exact_matches_checked, match_tuples, repos
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match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
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return match_tuples
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def search_repository_metadata( trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ):
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def search_repository_metadata( app, exact_matches_checked, tool_ids='', tool_names='', tool_versions='',
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workflow_names='', all_workflows=False ):
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sa_session=app.model.context.current
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match_tuples = []
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ok = True
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if tool_ids or tool_names or tool_versions:
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for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \
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.filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \
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.join( trans.model.Repository ) \
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.filter( and_( trans.model.Repository.table.c.deleted == False,
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trans.model.Repository.table.c.deprecated == False ) ):
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for repository_metadata in sa_session.query( app.model.RepositoryMetadata ) \
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.filter( app.model.RepositoryMetadata.table.c.includes_tools == True ) \
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.join( app.model.Repository ) \
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.filter( and_( app.model.Repository.table.c.deleted == False,
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app.model.Repository.table.c.deprecated == False ) ):
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metadata = repository_metadata.metadata
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if metadata:
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tools = metadata.get( 'tools', [] )
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@@ -140,11 +142,11 @@ def search_repository_metadata( trans, exact_matches_checked, tool_ids='', tool_
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else:
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ok = False
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elif workflow_names or all_workflows:
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for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \
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.filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \
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.join( trans.model.Repository ) \
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.filter( and_( trans.model.Repository.table.c.deleted == False,
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trans.model.Repository.table.c.deprecated == False ) ):
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for repository_metadata in sa_session.query( app.model.RepositoryMetadata ) \
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.filter( app.model.RepositoryMetadata.table.c.includes_workflows == True ) \
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.join( app.model.Repository ) \
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.filter( and_( app.model.Repository.table.c.deleted == False,
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app.model.Repository.table.c.deprecated == False ) ):
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metadata = repository_metadata.metadata
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if metadata:
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# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
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@@ -128,9 +128,9 @@ def get_platform_info_dict():
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platform_dict[ 'architecture' ] = machine.lower()
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return platform_dict
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def get_tool_dependency( trans, id ):
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def get_tool_dependency( app, id ):
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"""Get a tool_dependency from the database via id"""
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return trans.install_model.context.query( trans.install_model.ToolDependency ).get( trans.security.decode_id( id ) )
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return app.install_model.context.query( app.install_model.ToolDependency ).get( app.security.decode_id( id ) )
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def get_tool_dependency_by_name_type_repository( app, repository, name, type ):
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context = app.install_model.context
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