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commit/galaxy-central: greg: Fixes for administering tool dependencies associated with tool shed repositories installe dinto a Galaxy instance.
by Bitbucket 21 Dec '12

21 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0a3e4bc2b5a5/ changeset: 0a3e4bc2b5a5 user: greg date: 2012-12-21 02:48:11 summary: Fixes for administering tool dependencies associated with tool shed repositories installe dinto a Galaxy instance. affected #: 5 files diff -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 -r 0a3e4bc2b5a510820b8aba73b78433db810a3481 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -499,6 +499,8 @@ type = td_info_dict[ 'type' ] tool_dependency = get_tool_dependency_by_name_type_repository( trans, repository, name, type ) if tool_dependency: + td_info_dict[ 'repository_id' ] = repository.id + td_info_dict[ 'tool_dependency_id' ] = tool_dependency.id td_info_dict[ 'status' ] = str( tool_dependency.status ) val[ index ] = td_info_dict if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: @@ -510,12 +512,14 @@ version = val[ 'version' ] type = val[ 'type' ] tool_dependency = get_tool_dependency_by_name_version_type_repository( trans, repository, name, version, type ) - val[ 'status' ] = str( tool_dependency.status ) - if tool_dependency: - if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: - tool_dependencies[ td_key ] = val - else: - missing_tool_dependencies[ td_key ] = val + if tool_dependency: + val[ 'repository_id' ] = repository.id + val[ 'tool_dependency_id' ] = tool_dependency.id + val[ 'status' ] = str( tool_dependency.status ) + if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: + tool_dependencies[ td_key ] = val + else: + missing_tool_dependencies[ td_key ] = val else: tool_dependencies = None missing_tool_dependencies = None diff -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 -r 0a3e4bc2b5a510820b8aba73b78433db810a3481 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -135,8 +135,8 @@ description = 'click the name to browse the dependency installation directory' folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, + label='Installed tool dependencies', for_galaxy=True, - repository_id=repository_id , description=description, display_status=False ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder @@ -148,7 +148,6 @@ missing_tool_dependencies, label='Missing tool dependencies', for_galaxy=True, - repository_id=repository_id, description=description, display_status=True ) containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder @@ -220,7 +219,6 @@ folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=False, - repository_id=None, description=None, display_status=False ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder @@ -837,7 +835,7 @@ env_name = env_elem.get( 'name', None ) if env_name: requirements_dict [ 'name' ] = env_name - requirements_dict [ 'type' ] = 'environment variable' + requirements_dict [ 'type' ] = 'set_environment' if requirements_dict: if 'set_environment' in tool_dependencies_dict: tool_dependencies_dict[ 'set_environment' ].append( requirements_dict ) diff -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 -r 0a3e4bc2b5a510820b8aba73b78433db810a3481 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -98,7 +98,8 @@ class ToolDependency( object ): """Tool dependency object""" - def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None, ): + def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None, + tool_dependency_id=None ): self.id = id self.name = name self.version = version @@ -107,6 +108,7 @@ self.readme = readme self.installation_status = installation_status self.repository_id = repository_id + self.tool_dependency_id = tool_dependency_id class Workflow( object ): """Workflow object""" @@ -279,8 +281,7 @@ else: tools_root_folder = None return folder_id, tools_root_folder -def build_tool_dependencies_folder( folder_id, tool_dependencies, label='Installed tool dependencies', for_galaxy=False, repository_id=None, description=None, - display_status=False ): +def build_tool_dependencies_folder( folder_id, tool_dependencies, label='Tool dependencies', for_galaxy=False, description=None, display_status=False ): """Return a folder hierarchy containing tool dependencies.""" if tool_dependencies: tool_dependency_id = 0 @@ -298,8 +299,7 @@ tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', version='Version', - type='Type', - repository_id=repository_id ) + type='Type' ) if display_status: tool_dependency.installation_status = 'Status' else: @@ -308,8 +308,7 @@ tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', version='Version', - type='Type', - repository_id=repository_id ) + type='Type' ) if display_status: tool_dependency.installation_status = 'Status' folder.tool_dependencies.append( tool_dependency ) @@ -317,25 +316,30 @@ tool_dependency_id += 1 if dependency_key == 'set_environment': for set_environment_dict in requirements_dict: - name = set_environment_dict[ 'name' ] + name = set_environment_dict.get( 'name', None ) type = set_environment_dict[ 'type' ] + repository_id = set_environment_dict.get( 'repository_id', None ) + td_id = set_environment_dict.get( 'tool_dependency_id', None ) if display_status: - installation_status = set_environment_dict[ 'status' ] + installation_status = set_environment_dict.get( 'status', None ) else: installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, name=name, type=type, installation_status=installation_status, - repository_id=repository_id ) + repository_id=repository_id, + tool_dependency_id=td_id ) folder.tool_dependencies.append( tool_dependency ) else: name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] install_dir = requirements_dict.get( 'install_dir', None ) + repository_id = requirements_dict.get( 'repository_id', None ) + td_id = requirements_dict.get( 'tool_dependency_id', None ) if display_status: - installation_status = requirements_dict[ 'status' ] + installation_status = requirements_dict.get( 'status', None ) else: installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, @@ -344,7 +348,8 @@ type=type, install_dir=install_dir, installation_status=installation_status, - repository_id=repository_id ) + repository_id=repository_id, + tool_dependency_id=td_id ) folder.tool_dependencies.append( tool_dependency ) else: tool_dependencies_root_folder = None diff -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 -r 0a3e4bc2b5a510820b8aba73b78433db810a3481 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -430,17 +430,15 @@ <${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${tool_dependency.name | h} - %elif tool_dependency.repository_id: - %if not tool_dependency.installation_status: - ## tool_dependency.installation_status will be None if the status value in the database is 'Installed'. - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( tool_dependency.repository_id ) )}"> - ${tool_dependency.name | h} - </a> - %else: - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( tool_dependency.id ) )}"> - ${tool_dependency.name} - </a> - %endif + %elif trans.webapp.name == 'galaxy' and tool_dependency.tool_dependency_id and tool_dependency.repository_id and not tool_dependency.installation_status: + ## tool_dependency.installation_status will be None if the status value in the database is 'Installed'. + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.tool_dependency_id ), repository_id=trans.security.encode_id( tool_dependency.repository_id ) )}"> + ${tool_dependency.name | h} + </a> + %elif trans.webapp.name == 'galaxy' and tool_dependency.tool_dependency_id and tool_dependency.installation_status: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}"> + ${tool_dependency.name} + </a> %else: ${tool_dependency.name | h} %endif diff -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 -r 0a3e4bc2b5a510820b8aba73b78433db810a3481 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -62,9 +62,7 @@ self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0010 Repository With Tool Dependencies' ] ) category = test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' ) self.browse_category( category, strings_displayed=[ 'freebayes_0010' ] ) - self.preview_repository_in_tool_shed( 'freebayes_0010', common.test_user_1_name, strings_displayed=[ 'freebayes_0010', - 'Valid tools', - 'Installed tool dependencies' ] ) + self.preview_repository_in_tool_shed( 'freebayes_0010', common.test_user_1_name, strings_displayed=[ 'freebayes_0010', 'Valid tools', 'Tool dependencies' ] ) def test_0015_install_freebayes_repository( self ): '''Install the freebayes repository without installing tool dependencies.''' strings_displayed=[ 'set your tool_dependency_dir', 'can be automatically installed', 'Set the tool_dependency_dir' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Enhancements to tool shed containers to enable features when tool shed repositories are installed in Galaxy.
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c159eafdf9d3/ changeset: c159eafdf9d3 user: greg date: 2012-12-20 23:39:31 summary: Enhancements to tool shed containers to enable features when tool shed repositories are installed in Galaxy. affected #: 5 files diff -r 4971f90034e88ff9397adcc2cf406d20f09c2714 -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -493,20 +493,29 @@ missing_tool_dependencies = {} for td_key, val in all_tool_dependencies.items(): if td_key in [ 'set_environment' ]: - for td_info_dict in val: + for index, td_info_dict in enumerate( val ): name = td_info_dict[ 'name' ] version = None type = td_info_dict[ 'type' ] - tool_dependency = get_tool_dependency_by_name_type_repository( trans, repository, name, type ) + tool_dependency = get_tool_dependency_by_name_type_repository( trans, repository, name, type ) + if tool_dependency: + td_info_dict[ 'status' ] = str( tool_dependency.status ) + val[ index ] = td_info_dict + if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: + tool_dependencies[ td_key ] = val + else: + missing_tool_dependencies[ td_key ] = val else: name = val[ 'name' ] version = val[ 'version' ] type = val[ 'type' ] tool_dependency = get_tool_dependency_by_name_version_type_repository( trans, repository, name, version, type ) - if tool_dependency and tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: - tool_dependencies[ td_key ] = val - else: - missing_tool_dependencies[ td_key ] = val + val[ 'status' ] = str( tool_dependency.status ) + if tool_dependency: + if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: + tool_dependencies[ td_key ] = val + else: + missing_tool_dependencies[ td_key ] = val else: tool_dependencies = None missing_tool_dependencies = None diff -r 4971f90034e88ff9397adcc2cf406d20f09c2714 -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -87,6 +87,12 @@ tool_dependencies=None, valid_tools=None, workflows=None ) + # Some of the tool dependency folders will include links to display tool dependency information, and some of these links require the repository + # id. However we need to be careful because sometimes the repository object is None. + if repository: + repository_id = repository.id + else: + repository_id = None lock = threading.Lock() lock.acquire( True ) if tool_dependencies: @@ -125,12 +131,26 @@ containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder # Tool dependencies container. if tool_dependencies: - folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) + # We only want to display the Status column if the tool_dependency is missing. + description = 'click the name to browse the dependency installation directory' + folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, + tool_dependencies, + for_galaxy=True, + repository_id=repository_id , + description=description, + display_status=False ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder # Missing tool dependencies container. if missing_tool_dependencies: - folder_id, missing_tool_dependencies_root_folder = \ - container_util.build_tool_dependencies_folder( folder_id, missing_tool_dependencies, label='Missing tool dependencies', for_galaxy=True ) + description = 'click the name to install the missing dependency' + # We only want to display the Status column if the tool_dependency is missing. + folder_id, missing_tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, + missing_tool_dependencies, + label='Missing tool dependencies', + for_galaxy=True, + repository_id=repository_id, + description=description, + display_status=True ) containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder # Valid tools container. if valid_tools: @@ -197,7 +217,12 @@ # Tool dependencies container. if metadata and 'tool_dependencies' in metadata: tool_dependencies = metadata[ 'tool_dependencies' ] - folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=False ) + folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, + tool_dependencies, + for_galaxy=False, + repository_id=None, + description=None, + display_status=False ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder # Valid tools container. if metadata and 'tools' in metadata: @@ -2441,26 +2466,28 @@ return file_name def to_safe_string( text, to_html=True ): """Translates the characters in text to an html string""" - translated = [] - for c in text: - if c in VALID_CHARS: - translated.append( c ) - elif c in MAPPED_CHARS: - translated.append( MAPPED_CHARS[ c ] ) - elif c in [ '\n' ]: - if to_html: - translated.append( '<br/>' ) + if text: + translated = [] + for c in text: + if c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + elif c in [ '\n' ]: + if to_html: + translated.append( '<br/>' ) + else: + translated.append( c ) + elif c in [ '\r' ]: + continue + elif c in [ ' ', ' ' ]: + translated.append( c ) else: - translated.append( c ) - elif c in [ '\r' ]: - continue - elif c in [ ' ', ' ' ]: - translated.append( c ) - else: - translated.append( '' ) - if to_html: - str( markupsafe.escape( ''.join( translated ) ) ) - return ''.join( translated ) + translated.append( '' ) + if to_html: + str( markupsafe.escape( ''.join( translated ) ) ) + return ''.join( translated ) + return text def tool_shed_from_repository_clone_url( repository_clone_url ): return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def tool_shed_is_this_tool_shed( toolshed_base_url ): diff -r 4971f90034e88ff9397adcc2cf406d20f09c2714 -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -71,12 +71,13 @@ class RepositoryDependency( object ): """Repository dependency object""" - def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None ): + def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, installation_status=None ): self.id = id self.toolshed = toolshed self.repository_name = repository_name self.repository_owner = repository_owner self.changeset_revision = changeset_revision + self.installation_status = installation_status @property def listify( self ): return [ self.toolshed, self.repository_name, self.repository_owner, self.changeset_revision ] @@ -97,13 +98,15 @@ class ToolDependency( object ): """Tool dependency object""" - def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None ): + def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None, ): self.id = id self.name = name self.version = version self.type = type self.install_dir = install_dir self.readme = readme + self.installation_status = installation_status + self.repository_id = repository_id class Workflow( object ): """Workflow object""" @@ -115,7 +118,7 @@ self.format_version = format_version self.annotation = annotation -def build_datatypes_folder( folder_id, datatypes, label='Datatypes' ): +def build_datatypes_folder( folder_id, datatypes, label='Datatypes', description=None ): """Return a folder hierarchy containing datatypes.""" if datatypes: datatype_id = 0 @@ -123,6 +126,8 @@ datatypes_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 folder = Folder( id=folder_id, key='datatypes', label=label, parent=datatypes_root_folder ) + if description: + folder.description = description datatypes_root_folder.folders.append( folder ) # Insert a header row. datatype_id += 1 @@ -143,7 +148,7 @@ else: datatypes_root_folder = None return folder_id, datatypes_root_folder -def build_invalid_tools_folder( folder_id, invalid_tool_configs, changeset_revision, repository=None, label='Invalid tools' ): +def build_invalid_tools_folder( folder_id, invalid_tool_configs, changeset_revision, repository=None, label='Invalid tools', description=None ): """Return a folder hierarchy containing invalid tools.""" # TODO: Should we display invalid tools on the tool panel selection page when installing the repository into Galaxy? if invalid_tool_configs: @@ -152,6 +157,8 @@ invalid_tools_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 folder = Folder( id=folder_id, key='invalid_tools', label=label, parent=invalid_tools_root_folder ) + if description: + folder.description = description invalid_tools_root_folder.folders.append( folder ) for invalid_tool_config in invalid_tool_configs: invalid_tool_id += 1 @@ -167,7 +174,7 @@ else: invalid_tools_root_folder = None return folder_id, invalid_tools_root_folder -def build_readme_files_folder( folder_id, readme_files_dict, label='Readme files' ): +def build_readme_files_folder( folder_id, readme_files_dict, label='Readme files', description=None ): """Return a folder hierarchy containing readme text files.""" if readme_files_dict: multiple_readme_files = len( readme_files_dict ) > 1 @@ -177,6 +184,8 @@ if multiple_readme_files: folder_id += 1 readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) + if description: + readme_files_folder.description = description readme_files_root_folder.folders.append( readme_files_folder ) for readme_file_name, readme_file_text in readme_files_dict.items(): readme_id += 1 @@ -195,7 +204,7 @@ readme_files_root_folder = None return folder_id, readme_files_root_folder def build_repository_dependencies_folder( toolshed_base_url, repository_name, repository_owner, changeset_revision, folder_id, repository_dependencies, - label='Repository dependencies' ): + label='Repository dependencies', description=None ): """Return a folder hierarchy containing repository dependencies.""" if repository_dependencies: repository_dependency_id = 0 @@ -206,6 +215,8 @@ # Create the Repository dependencies folder and add it to the root folder. repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label, parent=repository_dependencies_root_folder ) + if description: + repository_dependencies_folder.description = description del repository_dependencies[ 'root_key' ] # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more repository_dependency keys. # We want the description value associated with the repository_dependencies_folder. @@ -268,7 +279,8 @@ else: tools_root_folder = None return folder_id, tools_root_folder -def build_tool_dependencies_folder( folder_id, tool_dependencies, label='Tool dependencies', for_galaxy=False ): +def build_tool_dependencies_folder( folder_id, tool_dependencies, label='Installed tool dependencies', for_galaxy=False, repository_id=None, description=None, + display_status=False ): """Return a folder hierarchy containing tool dependencies.""" if tool_dependencies: tool_dependency_id = 0 @@ -276,6 +288,8 @@ tool_dependencies_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 folder = Folder( id=folder_id, key='tool_dependencies', label=label, parent=tool_dependencies_root_folder ) + if description: + folder.description = description tool_dependencies_root_folder.folders.append( folder ) # Insert a header row. tool_dependency_id += 1 @@ -285,12 +299,19 @@ name='Name', version='Version', type='Type', - install_dir='Install directory' ) + repository_id=repository_id ) + if display_status: + tool_dependency.installation_status = 'Status' + else: + tool_dependency.install_dir = 'Install directory' else: tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', version='Version', - type='Type' ) + type='Type', + repository_id=repository_id ) + if display_status: + tool_dependency.installation_status = 'Status' folder.tool_dependencies.append( tool_dependency ) for dependency_key, requirements_dict in tool_dependencies.items(): tool_dependency_id += 1 @@ -298,25 +319,37 @@ for set_environment_dict in requirements_dict: name = set_environment_dict[ 'name' ] type = set_environment_dict[ 'type' ] + if display_status: + installation_status = set_environment_dict[ 'status' ] + else: + installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, name=name, - type=type ) + type=type, + installation_status=installation_status, + repository_id=repository_id ) folder.tool_dependencies.append( tool_dependency ) else: name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] install_dir = requirements_dict.get( 'install_dir', None ) + if display_status: + installation_status = requirements_dict[ 'status' ] + else: + installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, name=name, version=version, type=type, - install_dir=install_dir ) + install_dir=install_dir, + installation_status=installation_status, + repository_id=repository_id ) folder.tool_dependencies.append( tool_dependency ) else: tool_dependencies_root_folder = None return folder_id, tool_dependencies_root_folder -def build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ): +def build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows', description=None ): """Return a folder hierarchy containing invalid tools.""" if workflows: workflow_id = 0 @@ -324,6 +357,8 @@ workflows_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 folder = Folder( id=folder_id, key='workflows', label=label, parent=workflows_root_folder ) + if description: + folder.description = description workflows_root_folder.folders.append( folder ) # Insert a header row. workflow_id += 1 diff -r 4971f90034e88ff9397adcc2cf406d20f09c2714 -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -203,6 +203,12 @@ folder_label = str( folder.label ) if folder.datatypes: col_span_str = 'colspan="4"' + elif folder.label == 'Missing tool dependencies': + if folder.description: + folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) + else: + folder_label = "%s<i> - this repository's tools require handling of these missing dependencies</i>" % folder_label + col_span_str = 'colspan="5"' elif folder.label == 'Repository dependencies': if folder.description: folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) @@ -217,8 +223,11 @@ elif folder.invalid_tools: folder_label = "%s<i> - click the tool config file name to see why the tool is invalid</i>" % folder_label elif folder.tool_dependencies: - folder_label = "%s<i> - this repository's tools require handling of these dependencies</i>" % folder_label - col_span_str = 'colspan="3"' + if folder.description: + folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) + else: + folder_label = "%s<i> - this repository's tools require handling of these dependencies</i>" % folder_label + col_span_str = 'colspan="4"' elif folder.workflows: col_span_str = 'colspan="4"' %> @@ -418,7 +427,24 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <${cell_type} style="padding-left: ${pad+20}px;">${tool_dependency.name | h}</${cell_type}> + <${cell_type} style="padding-left: ${pad+20}px;"> + %if row_is_header: + ${tool_dependency.name | h} + %elif tool_dependency.repository_id: + %if not tool_dependency.installation_status: + ## tool_dependency.installation_status will be None if the status value in the database is 'Installed'. + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( tool_dependency.repository_id ) )}"> + ${tool_dependency.name | h} + </a> + %else: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( tool_dependency.id ) )}"> + ${tool_dependency.name} + </a> + %endif + %else: + ${tool_dependency.name | h} + %endif + </${cell_type}><${cell_type}><% if tool_dependency.version: @@ -432,6 +458,9 @@ %if tool_dependency.install_dir: <${cell_type}>${tool_dependency.install_dir | h}</${cell_type}> %endif + %if tool_dependency.installation_status not in [ 'Installed', None ]: + <${cell_type}>${tool_dependency.installation_status | h}</${cell_type}> + %endif </tr><% my_row = row_counter.count diff -r 4971f90034e88ff9397adcc2cf406d20f09c2714 -r c159eafdf9d3e97e12b7c9db53509f13842c5b96 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -62,7 +62,9 @@ self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0010 Repository With Tool Dependencies' ] ) category = test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' ) self.browse_category( category, strings_displayed=[ 'freebayes_0010' ] ) - self.preview_repository_in_tool_shed( 'freebayes_0010', common.test_user_1_name, strings_displayed=[ 'freebayes_0010', 'Valid tools', 'Tool dependencies' ] ) + self.preview_repository_in_tool_shed( 'freebayes_0010', common.test_user_1_name, strings_displayed=[ 'freebayes_0010', + 'Valid tools', + 'Installed tool dependencies' ] ) def test_0015_install_freebayes_repository( self ): '''Install the freebayes repository without installing tool dependencies.''' strings_displayed=[ 'set your tool_dependency_dir', 'can be automatically installed', 'Set the tool_dependency_dir' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Fix server error when attempting to install a repository that has already been installed.
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4971f90034e8/ changeset: 4971f90034e8 user: inithello date: 2012-12-20 22:33:19 summary: Fix server error when attempting to install a repository that has already been installed. affected #: 2 files diff -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 -r 4971f90034e88ff9397adcc2cf406d20f09c2714 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -223,6 +223,7 @@ message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " message += "<b>Repository Actions</b> pop-up menu. " if len( repo_info_dicts ) == 1: + created_or_updated_tool_shed_repositories.append( installed_tool_shed_repository ) return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message else: # A tool shed repository is being installed into a Galaxy instance for the first time. We may have the case where a repository diff -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 -r 4971f90034e88ff9397adcc2cf406d20f09c2714 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1138,6 +1138,7 @@ created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False ) if message and len( repo_info_dicts ) == 1: + installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ] message+= 'Click <a href="%s">here</a> to manage the repository. ' % \ ( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) ) return trans.response.send_redirect( web.url_for( controller='admin_toolshed', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: functional tests, tags: fix test_005_add_tag_to_history to check for tag using get_tagging_elt_async; twilltestcase: add get_tags (get_tagging_elt_async)
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3c4600ee9bdf/ changeset: 3c4600ee9bdf user: carlfeberhard date: 2012-12-20 21:20:42 summary: functional tests, tags: fix test_005_add_tag_to_history to check for tag using get_tagging_elt_async; twilltestcase: add get_tags (get_tagging_elt_async) affected #: 2 files diff -r 5d4372b6e2855a69758716fc20440071d3f19fbf -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2474,3 +2474,6 @@ def add_tag( self, item_id, item_class, context, new_tag ): self.visit_url( "%s/tag/add_tag_async?item_id=%s&item_class=%s&context=%s&new_tag=%s" % \ ( self.url, item_id, item_class, context, new_tag ) ) + def get_tags( self, item_id, item_class ): + self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" % \ + ( self.url, item_id, item_class ) ) diff -r 5d4372b6e2855a69758716fc20440071d3f19fbf -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 test/functional/test_tags.py --- a/test/functional/test_tags.py +++ b/test/functional/test_tags.py @@ -33,6 +33,7 @@ assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' global admin_user_private_role admin_user_private_role = get_private_role( admin_user ) + def test_005_add_tag_to_history( self ): """Testing adding a tag to a history""" # Logged in as admin_user @@ -45,7 +46,9 @@ 'History', 'history.mako', 'hello' ) - self.check_history_for_string( 'tags : {"hello"' ) + self.get_tags( self.security.encode_id( history1.id ), 'History' ) + self.check_page_for_string( 'tags : {"hello": ""}' ) + def test_010_add_tag_to_history_item( self ): """Testing adding a tag to a history item""" # Logged in as admin_user @@ -56,6 +59,7 @@ 'edit_attributes.mako', 'goodbye' ) self.check_hda_attribute_info( 'tags : {"goodbye"' ) + def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to to be valid""" # logged in as admin_user Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 20 Dec '12

20 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/690ea95aec34/ changeset: 690ea95aec34 user: inithello date: 2012-12-20 21:14:13 summary: Fix error reinstalling a repository when repo_info_dict is missing from the parameters. affected #: 1 file diff -r 5f3a470e75017b36e3fe37e5343043c551b7a2cd -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1374,7 +1374,6 @@ changeset_revision=tool_shed_repository.installed_changeset_revision ) else: repository_dependencies = None - repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) ) repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.installed_changeset_revision, https://bitbucket.org/galaxy/galaxy-central/changeset/5d4372b6e285/ changeset: 5d4372b6e285 user: inithello date: 2012-12-20 21:16:56 summary: Tool shed functional tests for reinstalling repositories and installing repositories with invalid tools. affected #: 10 files diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -16,8 +16,15 @@ sa_session.flush() def get_all_repositories(): return sa_session.query( model.Repository ).all() -def get_all_installed_repositories(): - return ga_session.query( galaxy.model.ToolShedRepository ).all() +def get_all_installed_repositories( actually_installed=False ): + if actually_installed: + return ga_session.query( galaxy.model.ToolShedRepository ) \ + .filter( and_( galaxy.model.ToolShedRepository.table.c.deleted == False, + galaxy.model.ToolShedRepository.table.c.uninstalled == False, + galaxy.model.ToolShedRepository.table.c.status == galaxy.model.ToolShedRepository.installation_status.INSTALLED ) ) \ + .all() + else: + return ga_session.query( galaxy.model.ToolShedRepository ).all() def get_category_by_name( name ): return sa_session.query( model.Category ) \ .filter( model.Category.table.c.name == name ) \ diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -196,6 +196,10 @@ tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) ) tc.submit( 'select_files_to_delete_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_galaxy_browse_repositories_page( self, strings_displayed=[], strings_not_displayed=[] ): + url = '/admin_toolshed/browse_repositories' + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def display_installed_repository_manage_page( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/manage_repository?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) @@ -392,7 +396,20 @@ tc.fv( "3", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def install_repository( self, name, owner, category_name, install_tool_dependencies=False, changeset_revision=None, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[] ): + def initiate_installation_process( self ): + html = self.last_page() + # Since the installation process is by necessity asynchronous, we have to get the parameters to 'manually' initiate the + # installation process. This regex will return the tool shed repository IDs in group(1), the encoded_kwd parameter in + # group(2), and the reinstalling flag in group(3) and pass them to the manage_repositories method in the Galaxy + # admin_toolshed controller. + install_parameters = re.search( 'initiate_repository_installation$ "([^"]+)", "([^"]+)", "([^"]+)" $;', html ) + iri_ids = install_parameters.group(1) + encoded_kwd = install_parameters.group(2) + reinstalling = install_parameters.group(3) + url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \ + ( iri_ids, encoded_kwd, reinstalling ) + self.visit_galaxy_url( url ) + def install_repository( self, name, owner, category_name, install_tool_dependencies=False, changeset_revision=None, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], **kwd ): if test_db_util.get_installed_repository_by_name_owner( name, owner ) is not None: return self.browse_tool_shed( url=self.url ) @@ -406,27 +423,16 @@ ( changeset_revision, repository_id, self.galaxy_url ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + form = tc.browser.get_form( 'select_tool_panel_section' ) if 'install_tool_dependencies' in self.last_page(): - form = tc.browser.get_form( 'select_tool_panel_section' ) checkbox = form.find_control( id="install_tool_dependencies" ) checkbox.disabled = False if install_tool_dependencies: checkbox.selected = True else: checkbox.selected = False - tc.submit( 'select_tool_panel_section_button' ) - html = self.last_page() - # Since the installation process is by necessity asynchronous, we have to get the parameters to 'manually' initiate the - # installation process. This regex will return the tool shed repository IDs in group(1), the encoded_kwd parameter in - # group(2), and the reinstalling flag in group(3) and pass them to the manage_repositories method in the Galaxy - # admin_toolshed controller. - install_parameters = re.search( 'initiate_repository_installation$ "([^"]+)", "([^"]+)", "([^"]+)" $;', html ) - iri_ids = install_parameters.group(1) - encoded_kwd = install_parameters.group(2) - reinstalling = install_parameters.group(3) - url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \ - ( iri_ids, encoded_kwd, reinstalling ) - self.visit_galaxy_url( url ) + self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) + self.initiate_installation_process() self.wait_for_repository_installation( repository, changeset_revision ) def load_invalid_tool_page( self, repository, tool_xml, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/load_invalid_tool?repository_id=%s&tool_config=%s&changeset_revision=%s' % \ @@ -451,6 +457,12 @@ self.visit_url( '/repository/preview_tools_in_changeset?repository_id=%s&changeset_revision=%s' % \ ( self.security.encode_id( repository.id ), changeset_revision ) ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def reinstall_repository( self, installed_repository ): + url = '/admin_toolshed/reinstall_repository?id=%s' % self.security.encode_id( installed_repository.id ) + self.visit_galaxy_url( url ) + self.initiate_installation_process() + tool_shed_repository = test_db_util.get_repository_by_name_and_owner( installed_repository.name, installed_repository.owner ) + self.wait_for_repository_installation( tool_shed_repository, installed_repository.installed_changeset_revision ) def repository_is_new( self, repository ): repo = hg.repository( ui.ui(), self.get_repo_path( repository ) ) tip_ctx = repo.changectx( repo.changelog.tip() ) @@ -495,6 +507,17 @@ def tip_has_metadata( self, repository ): tip = self.get_repository_tip( repository ) return test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, tip ) + def uninstall_repository( self, installed_repository, remove_from_disk=True ): + url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( installed_repository.id ) + self.visit_galaxy_url( url ) +# form = tc.browser.get_form( 'deactivate_or_uninstall_repository' ) + tc.fv ( 1, "remove_from_disk", '1' ) +# checkbox.readonly = False +# if remove_from_disk: +# checkbox.selected = True + tc.submit( 'deactivate_or_uninstall_repository_button' ) + strings_displayed = [ 'has been uninstalled', 'The repository named' ] + self.check_for_strings( strings_displayed, strings_not_displayed=[] ) def update_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/check_for_updates?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) @@ -521,15 +544,6 @@ self.reset_installed_repository_metadata( installed_repository ) new_metadata = installed_repository.metadata assert metadata == new_metadata, 'Metadata for installed repository %s differs after metadata reset.' % name - def verify_installed_repository_on_browse_page( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): - url = '/admin_toolshed/browse_repositories' - self.visit_galaxy_url( url ) - strings_displayed.extend( [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, - installed_repository.installed_changeset_revision ] ) - self.check_for_strings( strings_displayed, strings_not_displayed ) def verify_installed_repository_data_table_entries( self, data_tables=[] ): data_table = util.parse_xml( self.shed_tool_data_table_conf ) found = False diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_0070_invalid_tool.py --- /dev/null +++ b/test/tool_shed/functional/test_0070_invalid_tool.py @@ -0,0 +1,53 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +repository_name = 'freebayes_0070' +repository_description = "Galaxy's freebayes tool" +repository_long_description = "Long description of Galaxy's freebayes tool" + +class TestFreebayesRepository( ShedTwillTestCase ): + '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' + def test_0000_create_or_login_admin_user( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( name='Test 0070 Repository With Invalid Tool', description='Tests for a repository with an invalid tool.' ) + def test_0010_create_test_repository_and_upload_tool_xml( self ): + '''Create and populate a freebayes repository. After this test, it should contain one valid tool and one invalid tool.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + 'freebayes/freebayes.xml', + valid_tools_only=False, + strings_displayed=[], + commit_message='Uploaded the tool xml.' ) + self.upload_file( repository, + 'filtering/filtering_1.1.0.tar', + valid_tools_only=False, + strings_displayed=[], + commit_message='Uploaded the tool xml.', + remove_repo_files_not_in_tar='No' ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Valid tools', 'Invalid tools' ] ) + changeset_revision = self.get_repository_tip( repository ) + self.check_repository_tools_for_changeset_revision( repository, changeset_revision ) + self.check_repository_invalid_tools_for_changeset_revision( repository, + changeset_revision, + strings_displayed=[ 'requires an entry' ], + strings_not_displayed=[] ) diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_1000_install_basic_repository.py --- a/test/tool_shed/functional/test_1000_install_basic_repository.py +++ b/test/tool_shed/functional/test_1000_install_basic_repository.py @@ -51,9 +51,17 @@ '''Load the preview page for the filtering_0000 repository in the tool shed.''' self.preview_repository_in_tool_shed( 'filtering_0000', common.test_user_1_name, strings_displayed=[ 'filtering_0000', 'Valid tools' ] ) def test_0025_install_filtering_repository( self ): - self.install_repository( 'filtering_0000', common.test_user_1_name, 'Test 0000 Basic Repository Features 1' ) + self.install_repository( 'filtering_0000', + common.test_user_1_name, + 'Test 0000 Basic Repository Features 1', + new_tool_panel_section='test_1000' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) - self.verify_installed_repository_on_browse_page( installed_repository ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) self.verify_tool_metadata_for_installed_repository( installed_repository ) diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -70,9 +70,15 @@ common.test_user_1_name, 'Test 0010 Repository With Tool Dependencies', strings_displayed=strings_displayed, - install_tool_dependencies=False ) + install_tool_dependencies=False, + new_tool_panel_section='test_1010' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) - self.verify_installed_repository_on_browse_page( installed_repository ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -65,9 +65,18 @@ self.preview_repository_in_tool_shed( 'emboss_0020', common.test_user_1_name, strings_displayed=[ 'emboss_0020', 'Valid tools' ] ) def test_0015_install_emboss_repository( self ): '''Install the emboss repository without installing tool dependencies.''' - self.install_repository( 'emboss_0020', common.test_user_1_name, 'Test 0020 Basic Repository Dependencies', install_tool_dependencies=False ) + self.install_repository( 'emboss_0020', + common.test_user_1_name, + 'Test 0020 Basic Repository Dependencies', + install_tool_dependencies=False, + new_tool_panel_section='test_1020' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0020', common.test_user_1_name ) - self.verify_installed_repository_on_browse_page( installed_repository ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py @@ -107,9 +107,15 @@ common.test_user_1_name, 'Test 0030 Repository Dependency Revisions', changeset_revision=revisions[1], - install_tool_dependencies=False ) + install_tool_dependencies=False, + new_tool_panel_section='test_1030' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name ) - self.verify_installed_repository_on_browse_page( installed_repository ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_1070_invalid_tool.py --- /dev/null +++ b/test/tool_shed/functional/test_1070_invalid_tool.py @@ -0,0 +1,80 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +repository_name = 'freebayes_0070' +repository_description = "Galaxy's freebayes tool" +repository_long_description = "Long description of Galaxy's freebayes tool" + +class TestFreebayesRepository( ShedTwillTestCase ): + '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' + def test_0000_create_or_login_admin_user( self ): + """Create necessary user accounts and login as an admin user.""" + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email ) + assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_ensure_existence_of_repository_and_category( self ): + '''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.''' + self.create_category( name='Test 0070 Repository With Invalid Tool', + description='Tests for a repository with an invalid tool.' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'freebayes/freebayes.xml', + valid_tools_only=False, + commit_message='Uploaded the invalid tool xml.' ) + self.upload_file( repository, + 'filtering/filtering_1.1.0.tar', + valid_tools_only=False, + commit_message='Uploaded the valid tool xml.', + remove_repo_files_not_in_tar='No' ) + def test_0010_browse_tool_shed( self ): + """Browse the available tool sheds in this Galaxy instance and preview the freebayes repository.""" + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0070 Repository With Invalid Tool' ] ) + category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) + self.browse_category( category, strings_displayed=[ repository_name ] ) + self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=[ repository_name ] ) + def test_0015_install_freebayes_repository( self ): + '''Install the test repository without installing tool dependencies.''' + self.install_repository( repository_name, + common.test_user_1_name, + 'Test 0070 Repository With Invalid Tool', + install_tool_dependencies=False, + new_tool_panel_section='test_1070' ) + installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + self.display_installed_repository_manage_page( installed_repository, + strings_displayed=[ 'simple expressions', 'Invalid tools' ], + strings_not_displayed=[ 'variant detector' ] ) + self.verify_tool_metadata_for_installed_repository( installed_repository ) + self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] ) + assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % installed_repository.name + def test_0020_verify_installed_repository_metadata( self ): + '''Verify that resetting the metadata on an installed repository does not change the metadata.''' + self.verify_installed_repository_metadata_unchanged( repository_name, common.test_user_1_name ) diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py --- /dev/null +++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -0,0 +1,96 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +class BasicToolShedFeatures( ShedTwillTestCase ): + '''Test installing a basic repository.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email ) + assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user ) + def test_0005_ensure_repositories_and_categories_exist( self ): + '''Create the 0000 category and upload the filtering repository to the tool shed, if necessary.''' + category = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' ) + self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name='filtering_0000', + description="Galaxy's filtering tool", + long_description="Long description of Galaxy's filtering tool", + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ) ) + if self.repository_is_new( repository ): + self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) + self.upload_file( repository, 'filtering/filtering_0000.txt', commit_message="Uploaded readme for 1.1.0", remove_repo_files_not_in_tar='No' ) + self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) + self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme for 2.2.0", remove_repo_files_not_in_tar='No' ) + def test_0010_install_filtering_repository( self ): + '''Install the filtering repository into the Galaxy instance.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( 'filtering_0000', + common.test_user_1_name, + 'Test 0000 Basic Repository Features 1', + new_tool_panel_section='test_1000' ) + installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + def test_0015_uninstall_filtering_repository( self ): + '''Uninstall the filtering repository.''' + installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) + old_metadata = installed_repository.metadata + self.uninstall_repository( installed_repository, remove_from_disk=True ) + strings_not_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + def test_0020_reinstall_filtering_repository( self ): + '''Reinstall the filtering repository.''' + installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) + self.reinstall_repository( installed_repository ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + self.display_installed_repository_manage_page( installed_repository, + strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + self.verify_tool_metadata_for_installed_repository( installed_repository ) + def test_0025_deactivate_filtering_repository( self ): + '''Deactivate the filtering repository without removing it from disk.''' + installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) + self.uninstall_repository( installed_repository, remove_from_disk=False ) + strings_not_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + def test_0030_reactivate_filtering_repository( self ): + '''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.''' + installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) + self.reinstall_repository( installed_repository ) + strings_displayed = [ installed_repository.name, + installed_repository.description, + installed_repository.owner, + installed_repository.tool_shed, + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + self.display_installed_repository_manage_page( installed_repository, + strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + self.verify_tool_metadata_for_installed_repository( installed_repository ) diff -r 690ea95aec34dd0aaaba06f016d2468ea81f83e1 -r 5d4372b6e2855a69758716fc20440071d3f19fbf test/tool_shed/functional/test_1300_reset_all_metadata.py --- a/test/tool_shed/functional/test_1300_reset_all_metadata.py +++ b/test/tool_shed/functional/test_1300_reset_all_metadata.py @@ -258,7 +258,7 @@ def test_0015_reset_metadata_on_all_repositories( self ): '''Reset metadata on all repositories, then verify that it has not changed.''' repository_metadata = dict() - repositories = test_db_util.get_all_installed_repositories() + repositories = test_db_util.get_all_installed_repositories( actually_installed=True ) for repository in repositories: repository_metadata[ self.security.encode_id( repository.id ) ] = repository.metadata self.reset_metadata_on_selected_installed_repositories( repository_metadata.keys() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for handling tool dependency installation into a Galaxy instance.
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5f3a470e7501/ changeset: 5f3a470e7501 user: greg date: 2012-12-20 20:26:27 summary: Fixes for handling tool dependency installation into a Galaxy instance. affected #: 2 files diff -r 276c47b70c285fe9bee6aef86e65ca9463b661ae -r 5f3a470e75017b36e3fe37e5343043c551b7a2cd lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -79,7 +79,14 @@ invalid_tools, missing_tool_dependencies, readme_files_dict, repository_dependencies, tool_dependencies, valid_tools, workflows ): """Return a dictionary of containers for the received repository's dependencies and readme files for display during installation to Galaxy.""" - containers_dict = dict( readme_files=None, repository_dependencies=None, tool_dependencies=None ) + containers_dict = dict( datatypes=None, + invalid_tools=None, + missing_tool_dependencies=None, + readme_files=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) lock = threading.Lock() lock.acquire( True ) if tool_dependencies: diff -r 276c47b70c285fe9bee6aef86e65ca9463b661ae -r 5f3a470e75017b36e3fe37e5343043c551b7a2cd lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1258,17 +1258,6 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) - log.debug("PPPPP In prepare_for_install, containers_dict: %s" % str( containers_dict )) - """ - PPPPP In prepare_for_install, - containers_dict: - {'repository_dependencies': None, - 'missing_tool_dependencies': <galaxy.webapps.community.util.container_util.Folder object at 0x108a56f0>, - 'readme_files': None, - 'tool_dependencies': None} - FAIL - - """ return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, @@ -1538,9 +1527,10 @@ valid_tools = metadata.get( 'tools', None ) workflows = metadata.get( 'workflows', None ) # All tool dependencies will be considered missing since we are reinstalling the repository. - for td in tool_dependencies: - missing_tool_dependencies.append( td ) - tool_dependencies = None + if tool_dependencies: + for td in tool_dependencies: + missing_tool_dependencies.append( td ) + tool_dependencies = None containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, repository_name=tool_shed_repository.name, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: expose_api: add Cache-Control response headers to prevent some browsers from caching api calls
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/276c47b70c28/ changeset: 276c47b70c28 user: carlfeberhard date: 2012-12-20 19:42:45 summary: expose_api: add Cache-Control response headers to prevent some browsers from caching api calls affected #: 1 file diff -r 1073bded37116da144e4e292462346fb7b035bca -r 276c47b70c285fe9bee6aef86e65ca9463b661ae lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -155,6 +155,8 @@ error_message = 'Your request did not appear to be valid JSON, please consult the API documentation' return error trans.response.set_content_type( "application/json" ) + # send 'do not cache' headers to handle IE's caching of ajax get responses + trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store" # Perform api_run_as processing, possibly changing identity if 'payload' in kwargs and 'run_as' in kwargs['payload']: if not trans.user_can_do_run_as(): 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: pack scripts
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1073bded3711/ changeset: 1073bded3711 user: carlfeberhard date: 2012-12-20 18:35:09 summary: pack scripts affected #: 3 files diff -r a53fe9c9395621e0c9376ee7109274612f735cb9 -r 1073bded37116da144e4e292462346fb7b035bca 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.RelationalModel.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){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;function e(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this._save();return this},deleteKey:function(j){delete i[j];this._save();return this},_save:function(){return h._save()},toString:function(){return("StorageRecursionHelper("+i+")")}}}var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);jQuery.extend(f,{_save:function(h){return c(g,f.get())},destroy:function(){return a(g)},toString:function(){return"PersistantStorage("+g+")"}});return f}; \ No newline at end of file +var BaseModel=Backbone.RelationalModel.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 GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;function e(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this._save();return this},deleteKey:function(j){delete i[j];this._save();return this},_save:function(){return h._save()},toString:function(){return("StorageRecursionHelper("+i+")")}}}var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);jQuery.extend(f,{_save:function(h){return c(g,f.get())},destroy:function(){return a(g)},toString:function(){return"PersistantStorage("+g+")"}});return f}; \ No newline at end of file diff -r a53fe9c9395621e0c9376ee7109274612f735cb9 -r 1073bded37116da144e4e292462346fb7b035bca static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",b,a,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file diff -r a53fe9c9395621e0c9376ee7109274612f735cb9 -r 1073bded37116da144e4e292462346fb7b035bca 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:hidden",this.render,this);this.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(c.get("id"))}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("state:ready",function(c,d,b){if((!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(c.get("id"))}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ 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: base-mvc: fix to handle IE console methods being objects; history panel: handle workflow hide on finish using state:ready event
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a53fe9c93956/ changeset: a53fe9c93956 user: carlfeberhard date: 2012-12-20 18:25:09 summary: base-mvc: fix to handle IE console methods being objects; history panel: handle workflow hide on finish using state:ready event affected #: 3 files diff -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 -r a53fe9c9395621e0c9376ee7109274612f735cb9 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -78,7 +78,11 @@ */ log : function(){ if( this.logger ){ - return this.logger.log.apply( this.logger, arguments ); + var log = this.logger.log; + if( typeof this.logger.log == 'object' ){ + log = Function.prototype.bind.call( this.logger.log, this.logger ); + } + return log.apply( this.logger, arguments ); } return undefined; } diff -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 -r a53fe9c9395621e0c9376ee7109274612f735cb9 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -82,7 +82,7 @@ this.on( 'change:state', function( currModel, newState ){ this.log( this + ' has changed state:', currModel, newState ); if( this.inReadyState() ){ - this.trigger( 'state:ready', this.get( 'id' ), newState, this.previous( 'state' ), currModel ); + this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); diff -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 -r a53fe9c9395621e0c9376ee7109274612f735cb9 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -5,55 +5,6 @@ Backbone.js implementation of history panel TODO: - refactoring on for_editing: - uhoh: purge link in warning message in history_common.mako conditional on trans.app.config.allow_user_dataset_purge - bug: rerun still doesn't take encoded ids - - anon user, mako template init: - BUG: shouldn't have tag/anno buttons (on hdas) - Check for user in hdaView somehow - - logged in, mako template: - bug: rename not being changed locally - render() shows old name, refresh: new name - TODO: editable text to MV, might also just use REST.update on history - BUG: meter is not updating RELIABLY on change:nice_size - BUG: am able to start upload even if over quota - 'runs' forever - bug: quotaMeter bar rendering square in chrome - - from loadFromApi: - - fixed: - BUG: not loading deleted datasets - FIXED: history_contents, show: state_ids returns all ids now (incl. deleted) - BUG: upload, history size, doesn't change - FIXED: using change:nice_size to trigger re-render of history size - BUG: delete uploading hda - now in state 'discarded'! ...new state to handle - FIXED: handled state - BUG: historyItem, error'd ds show display, download? - FIXED: removed - bug: loading hdas (alt_hist) - FIXED: added anon user api request ( trans.user == None and trans.history.id == requested id ) - bug: quota meter not updating on upload/tool run - FIXED: quotaMeter now listens for 'state:ready' from glx_history in alternate_history.mako - bug: use of new HDACollection with event listener in init doesn't die...keeps reporting - FIXED: change getVisible to return an array - BUG: history, broken intial hist state (running, updater, etc.) - ??: doesn't seem to happen anymore - BUG: collapse all should remove all expanded from storage - FIXED: hideAllItemBodies now resets storage.expandedItems - BUG: historyItem, shouldn't allow tag, annotate, peek on purged datasets - FIXED: ok state now shows only: info, rerun - BUG: history?, some ids aren't returning encoded... - FIXED:??? - BUG: history, showing deleted ds - FIXED - UGH: historyItems have to be decorated with history_ids (api/histories/:history_id/contents/:id) - FIXED by adding history_id to history_contents.show - BUG: history, if hist has err'd ds, hist has perm state 'error', updater on following ds's doesn't run - FIXED by reordering history state from ds' states here and histories - BUG: history, broken annotation on reload (can't get thru api (sets fine, tho)) - FIXED: get thru api for now - replication: show_deleted/hidden: use storage @@ -61,9 +12,6 @@ need urls change template move histview fadein/out in render to app? - don't draw body until it's first expand event - localize all - ?: render url templates on init or render? ?: history, annotation won't accept unicode RESTful: @@ -167,13 +115,11 @@ //TODO??: purged //TODO??: could be more selective here this.model.hdas.bind( 'change:deleted', this.handleHdaDeletionChange, this ); - this.model.hdas.bind( 'change:hidden', this.render, this ); // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, // then: remove it from the collection if the panel is set to NOT show hidden datasets - this.model.hdas.bind( 'change:state', function( hda, newState, changedList ){ - if( ( hda.inReadyState() ) - && ( !hda.get( 'visible' ) ) + this.model.hdas.bind( 'state:ready', function( hda, newState, oldState ){ + if( ( !hda.get( 'visible' ) ) && ( !this.storage.get( 'show_hidden' ) ) ){ this.removeHdaView( hda.get( 'id' ) ); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fixes for handling tool dependencies and missing tool dependencies for installed tool shed repositories and tose being installed.
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/34b8a00ea301/ changeset: 34b8a00ea301 user: greg date: 2012-12-20 16:44:45 summary: Fixes for handling tool dependencies and missing tool dependencies for installed tool shed repositories and tose being installed. affected #: 3 files diff -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1749,14 +1749,31 @@ relative_install_dir = None shed_config_dict = repository.get_shed_config_dict( app ) if not shed_config_dict: - #just pick a semi-random shed config + # Just pick a semi-random shed config. for shed_config_dict in app.toolbox.shed_tool_confs: - if ( repository.dist_to_shed and shed_config_dict['config_filename'] == app.config.migrated_tools_config ) or ( not repository.dist_to_shed and shed_config_dict['config_filename'] != app.config.migrated_tools_config ): + if ( repository.dist_to_shed and shed_config_dict[ 'config_filename' ] == app.config.migrated_tools_config ) \ + or ( not repository.dist_to_shed and shed_config_dict[ 'config_filename' ] != app.config.migrated_tools_config ): break shed_tool_conf = shed_config_dict[ 'config_filename' ] tool_path = shed_config_dict[ 'tool_path' ] relative_install_dir = partial_install_dir return shed_tool_conf, tool_path, relative_install_dir +def get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ): + """ + Return the tool_path config setting for the received shed_tool_conf file by searching the tool box's in-memory list of shed_tool_confs for the + dictionary whose config_filename key has a value matching the received shed_tool_conf. + """ + for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: + config_filename = shed_tool_conf_dict[ 'config_filename' ] + if config_filename == shed_tool_conf: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + break + else: + file_name = strip_path( config_filename ) + if file_name == shed_tool_conf: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + break + return tool_path def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current diff -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -898,7 +898,7 @@ repository_dependencies_dict_for_display[ 'root_key' ] = root_key repository_dependencies_dict_for_display[ root_key ] = rd_tups repository_dependencies_dict_for_display[ 'description' ] = repository_dependencies[ 'description' ] - all_tool_dependencies = metadata.get( 'tool_dependencies', None ) + all_tool_dependencies = metadata.get( 'tool_dependencies', None ) tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ) valid_tools = metadata.get( 'tools', None ) workflows = metadata.get( 'workflows', None ) @@ -1126,7 +1126,7 @@ if ( not includes_tools and not includes_repository_dependencies ) or \ ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) - if includes_tools: + if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) shed_tool_conf = kwd[ 'shed_tool_conf' ] else: @@ -1134,17 +1134,7 @@ # If installing a repository that includes no tools, get the relative tool_path from the file to which the migrated_tools_config # setting points. shed_tool_conf = trans.app.config.migrated_tools_config - # Get the tool path by searching the list of shed_tool_confs for the dictionary that contains the information about shed_tool_conf. - for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: - config_filename = shed_tool_conf_dict[ 'config_filename' ] - if config_filename == shed_tool_conf: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - break - else: - file_name = suc.strip_path( config_filename ) - if file_name == shed_tool_conf: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - break + tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False ) if message and len( repo_info_dicts ) == 1: @@ -1232,6 +1222,8 @@ raw_text = response.read() response.close() readme_files_dict = from_json_string( raw_text ) + # Since we are installing a new repository, no tool dependencies will be considered "missing". Most of the repository contents + # are set to None since we don't yet know what they are. containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, repository_name=name, @@ -1247,7 +1239,13 @@ valid_tools=None, workflows=None ) else: - containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None ) + containers_dict = dict( datatypes=None, + invalid_tools=None, + readme_files_dict=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) # Handle tool dependencies chack box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: @@ -1260,6 +1258,17 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) + log.debug("PPPPP In prepare_for_install, containers_dict: %s" % str( containers_dict )) + """ + PPPPP In prepare_for_install, + containers_dict: + {'repository_dependencies': None, + 'missing_tool_dependencies': <galaxy.webapps.community.util.container_util.Folder object at 0x108a56f0>, + 'readme_files': None, + 'tool_dependencies': None} + FAIL + + """ return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, @@ -1456,6 +1465,7 @@ includes_repository_dependencies = True else: includes_repository_dependencies = False + includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.installed_changeset_revision, @@ -1527,6 +1537,10 @@ all_tool_dependencies ) valid_tools = metadata.get( 'tools', None ) workflows = metadata.get( 'workflows', None ) + # All tool dependencies will be considered missing since we are reinstalling the repository. + for td in tool_dependencies: + missing_tool_dependencies.append( td ) + tool_dependencies = None containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, repository_name=tool_shed_repository.name, @@ -1538,16 +1552,22 @@ missing_tool_dependencies=missing_tool_dependencies, readme_files_dict=readme_files_dict, repository_dependencies=repository_dependencies, - tool_dependencies=tool_dependencies, + tool_dependencies=missing_tool_dependencies, valid_tools=valid_tools, workflows=workflows ) else: - containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None ) + containers_dict = dict( datatypes=None, + invalid_tools=None, + readme_files_dict=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: - if tool_shed_repository.includes_tool_dependencies: + if includes_tool_dependencies: message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. " status = "warning" diff -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -509,7 +509,7 @@ </div></div> %endif - %if repository_dependencies_root_folder or tool_dependencies_root_folder: + %if repository_dependencies_root_folder or tool_dependencies_root_folder or missing_tool_dependencies_root_folder: <div class="toolForm"><div class="toolFormTitle">Dependencies of this repository</div><div class="toolFormBody"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for resintalling a single tool shed repository and fix for displaying the contents of an installed tool shed repository in Galaxy.
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8c3ad449b21d/ changeset: 8c3ad449b21d user: greg date: 2012-12-20 01:39:50 summary: Fix for resintalling a single tool shed repository and fix for displaying the contents of an installed tool shed repository in Galaxy. affected #: 2 files diff -r ddff35a4a9ab3cf22dad10c3b413f919d8d68022 -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -80,69 +80,68 @@ valid_tools, workflows ): """Return a dictionary of containers for the received repository's dependencies and readme files for display during installation to Galaxy.""" containers_dict = dict( readme_files=None, repository_dependencies=None, tool_dependencies=None ) - if readme_files_dict or repository_dependencies or tool_dependencies: - lock = threading.Lock() - lock.acquire( True ) + lock = threading.Lock() + lock.acquire( True ) + if tool_dependencies: + # Add the install_dir attribute to the tool_dependencies. + tool_dependencies = add_installation_directories_to_tool_dependencies( trans, + repository_name, + repository_owner, + changeset_revision, + tool_dependencies ) + try: + folder_id = 0 + # Datatypes container. + if datatypes: + folder_id, datatypes_root_folder = container_util.build_datatypes_folder( folder_id, datatypes ) + containers_dict[ 'datatypes' ] = datatypes_root_folder + # Invalid tools container. + if invalid_tools: + folder_id, invalid_tools_root_folder = container_util.build_invalid_tools_folder( folder_id, + invalid_tools, + changeset_revision, + repository=repository, + label='Invalid tools' ) + containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder + # Readme files container. + if readme_files_dict: + folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) + containers_dict[ 'readme_files' ] = readme_files_root_folder + # Repository dependencies container. + if repository_dependencies: + folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, + repository_name=repository_name, + repository_owner=repository_owner, + changeset_revision=changeset_revision, + folder_id=folder_id, + repository_dependencies=repository_dependencies ) + containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + # Tool dependencies container. if tool_dependencies: - # Add the install_dir attribute to the tool_dependencies. - tool_dependencies = add_installation_directories_to_tool_dependencies( trans, - repository_name, - repository_owner, - changeset_revision, - tool_dependencies ) - try: - folder_id = 0 - # Datatypes container. - if datatypes: - folder_id, datatypes_root_folder = container_util.build_datatypes_folder( folder_id, datatypes ) - containers_dict[ 'datatypes' ] = datatypes_root_folder - # Invalid tools container. - if invalid_tools: - folder_id, invalid_tools_root_folder = container_util.build_invalid_tools_folder( folder_id, - invalid_tools, - changeset_revision, - repository=repository, - label='Invalid tools' ) - containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder - # Readme files container. - if readme_files_dict: - folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) - containers_dict[ 'readme_files' ] = readme_files_root_folder - # Repository dependencies container. - if repository_dependencies: - folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, - repository_name=repository_name, - repository_owner=repository_owner, - changeset_revision=changeset_revision, - folder_id=folder_id, - repository_dependencies=repository_dependencies ) - containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder - # Tool dependencies container. - if tool_dependencies: - folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) - containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder - # Missing tool dependencies container. - if missing_tool_dependencies: - folder_id, missing_tool_dependencies_root_folder = \ - container_util.build_tool_dependencies_folder( folder_id, missing_tool_dependencies, label='Missing tool dependencies', for_galaxy=True ) - containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder - # Valid tools container. - if valid_tools: - folder_id, valid_tools_root_folder = container_util.build_tools_folder( folder_id, - valid_tools, - repository, - changeset_revision, - label='Valid tools', - description='click the name to inspect the tool metadata' ) - containers_dict[ 'valid_tools' ] = valid_tools_root_folder - # Workflows container. - if workflows: - folder_id, workflows_root_folder = container_util.build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) - containers_dict[ 'workflows' ] = workflows_root_folder - except Exception, e: - log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) ) - finally: - lock.release() + folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) + containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + # Missing tool dependencies container. + if missing_tool_dependencies: + folder_id, missing_tool_dependencies_root_folder = \ + container_util.build_tool_dependencies_folder( folder_id, missing_tool_dependencies, label='Missing tool dependencies', for_galaxy=True ) + containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder + # Valid tools container. + if valid_tools: + folder_id, valid_tools_root_folder = container_util.build_tools_folder( folder_id, + valid_tools, + repository, + changeset_revision, + label='Valid tools', + description='click the name to inspect the tool metadata' ) + containers_dict[ 'valid_tools' ] = valid_tools_root_folder + # Workflows container. + if workflows: + folder_id, workflows_root_folder = container_util.build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) + containers_dict[ 'workflows' ] = workflows_root_folder + except Exception, e: + log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) ) + finally: + lock.release() return containers_dict def build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata ): """Return a dictionary of containers for the received repository's dependencies and contents for display in the tool shed.""" diff -r ddff35a4a9ab3cf22dad10c3b413f919d8d68022 -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1365,10 +1365,7 @@ ctx_rev = suc.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) repo_info_dicts = [] repo_info_dict = kwd.get( 'repo_info_dict', None ) - if repo_info_dict: - # The repo_info_dict should be encoded. - repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) - else: + if not repo_info_dict: # Entering this if block used to happen only if the tool_shed_repository does not include any valid tools. After repository dependencies # were introduced, it may never happen, but we'll keep the block just in case. if install_repository_dependencies: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for retrieving tool dependencies and missing tool dependencies for display in Galaxy.
by Bitbucket 20 Dec '12

20 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ddff35a4a9ab/ changeset: ddff35a4a9ab user: greg date: 2012-12-20 00:59:07 summary: Fix for retrieving tool dependencies and missing tool dependencies for display in Galaxy. affected #: 1 file diff -r 10b6b20bfa0731813d17a0d246f5f57c7f5098da -r ddff35a4a9ab3cf22dad10c3b413f919d8d68022 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -490,15 +490,22 @@ if all_tool_dependencies: tool_dependencies = {} missing_tool_dependencies = {} - for td_key, td_info_dict in all_tool_dependencies.items(): - name = td_info_dict[ 'name' ] - version = td_info_dict[ 'version' ] - type = td_info_dict[ 'type' ] - tool_dependency = get_tool_dependency_by_name_version_type_repository( trans, repository, name, version, type ) - if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: - tool_dependencies[ td_key ] = td_info_dict + for td_key, val in all_tool_dependencies.items(): + if td_key in [ 'set_environment' ]: + for td_info_dict in val: + name = td_info_dict[ 'name' ] + version = None + type = td_info_dict[ 'type' ] + tool_dependency = get_tool_dependency_by_name_type_repository( trans, repository, name, type ) else: - missing_tool_dependencies[ td_key ] = td_info_dict + name = val[ 'name' ] + version = val[ 'version' ] + type = val[ 'type' ] + tool_dependency = get_tool_dependency_by_name_version_type_repository( trans, repository, name, version, type ) + if tool_dependency and tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: + tool_dependencies[ td_key ] = val + else: + missing_tool_dependencies[ td_key ] = val else: tool_dependencies = None missing_tool_dependencies = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history_panel: do not re-render panel when an hda is deleted
by Bitbucket 19 Dec '12

19 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/10b6b20bfa07/ changeset: 10b6b20bfa07 user: carlfeberhard date: 2012-12-19 23:08:21 summary: history_panel: do not re-render panel when an hda is deleted affected #: 4 files diff -r cfab4734097b388776035fdd2741ccf6a370b95c -r 10b6b20bfa0731813d17a0d246f5f57c7f5098da static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -546,9 +546,12 @@ } }, - - remove : function(){ - + remove : function( callback ){ + var hdaView = this; + this.$el.fadeOut( 'fast', function(){ + hdaView.$el.remove(); + if( callback ){ callback(); } + }); }, // ......................................................................... MISC diff -r cfab4734097b388776035fdd2741ccf6a370b95c -r 10b6b20bfa0731813d17a0d246f5f57c7f5098da static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -166,20 +166,18 @@ // when a hda model is (un)deleted or (un)hidden, re-render entirely //TODO??: purged //TODO??: could be more selective here - this.model.hdas.bind( 'change:deleted change:hidden', this.render, this ); + this.model.hdas.bind( 'change:deleted', this.handleHdaDeletionChange, this ); + this.model.hdas.bind( 'change:hidden', this.render, this ); // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, // then: remove it from the collection if the panel is set to NOT show hidden datasets - this.model.hdas.bind( 'change:state', - function( hda, newState, changedList ){ - //TODO: magic string here - somehow use HDA.states - if( ( hda.inReadyState() ) - && ( !hda.get( 'visible' ) ) - && ( !this.storage.get( 'show_hidden' ) ) ){ - this.removeHda( hda ); - } - }, - this ); + this.model.hdas.bind( 'change:state', function( hda, newState, changedList ){ + if( ( hda.inReadyState() ) + && ( !hda.get( 'visible' ) ) + && ( !this.storage.get( 'show_hidden' ) ) ){ + this.removeHdaView( hda.get( 'id' ) ); + } + }, this ); //this.bind( 'all', function(){ // this.log( arguments ); @@ -253,16 +251,27 @@ this.render(); }, - /** Remove a view from the panel and the assoc. model from the collection - * @param {HistoryDataAssociation} the hda to remove + /** If this hda is deleted and we're not showing deleted hdas, remove the view + * @param {HistoryDataAssociation} the hda to check */ - removeHda : function( hdaModel, callback ){ - var hdaView = this.hdaViews[ hdaModel.get( 'id' ) ]; - hdaView.$el.fadeOut( 'fast', function(){ - hdaView.$el.remove(); - if( callback ){ callback(); } - }); - this.model.hdas.remove( hdaModel ); + handleHdaDeletionChange : function( hda ){ + if( hda.get( 'deleted' ) && !this.storage.get( 'show_deleted' ) ){ + this.removeHdaView( hda.get( 'id' ) ); + } // otherwise, the hdaView rendering should handle it + }, + + /** Remove a view from the panel and if the panel is now empty, re-render + * @param {Int} the id of the hdaView to remove + */ + removeHdaView : function( id, callback ){ + var hdaView = this.hdaViews[ id ]; + if( !hdaView ){ return; } + + hdaView.remove( callback ); + delete this.hdaViews[ id ]; + if( _.isEmpty( this.hdaViews ) ){ + this.render(); + } }, // ......................................................................... RENDERING diff -r cfab4734097b388776035fdd2741ccf6a370b95c -r 10b6b20bfa0731813d17a0d246f5f57c7f5098da 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 @@ -var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(){},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r cfab4734097b388776035fdd2741ccf6a370b95c -r 10b6b20bfa0731813d17a0d246f5f57c7f5098da 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted change:hidden",this.render,this);this.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHda(c)}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},removeHda:function(a,c){var b=this.hdaViews[a.get("id")];b.$el.fadeOut("fast",function(){b.$el.remove();if(c){c()}});this.model.hdas.remove(a)},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:hidden",this.render,this);this.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(c.get("id"))}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ 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: inithello: Fix for displaying an installed repository that includes one or more readme files.
by Bitbucket 19 Dec '12

19 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cfab4734097b/ changeset: cfab4734097b user: inithello date: 2012-12-19 22:48:09 summary: Fix for displaying an installed repository that includes one or more readme files. affected #: 3 files diff -r 759d96f950b8825bcce157cdf5efbabaa0221b11 -r cfab4734097b388776035fdd2741ccf6a370b95c lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -57,13 +57,16 @@ requirements_dict[ 'install_dir' ] = install_dir tool_dependencies[ dependency_key ] = requirements_dict return tool_dependencies -def build_readme_files_dict( metadata ): +def build_readme_files_dict( metadata, tool_path=None ): """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received repository_metadata.""" readme_files_dict = {} if metadata and 'readme_files' in metadata: for relative_path_to_readme_file in metadata[ 'readme_files' ]: readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ] - full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file ) + if tool_path: + full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) ) + else: + full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file ) try: f = open( full_path_to_readme_file, 'r' ) text = f.read() @@ -103,7 +106,7 @@ containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder # Readme files container. if readme_files_dict: - folder_id, readme_files_root_folder = build_readme_files_folder( folder_id, readme_files_dict ) + folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) containers_dict[ 'readme_files' ] = readme_files_root_folder # Repository dependencies container. if repository_dependencies: diff -r 759d96f950b8825bcce157cdf5efbabaa0221b11 -r cfab4734097b388776035fdd2741ccf6a370b95c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -881,7 +881,7 @@ datatypes = metadata.get( 'datatypes', None ) invalid_tools = metadata.get( 'invalid_tools', None ) if repository.has_readme_files: - readme_files_dict = suc.build_readme_files_dict( repository.metadata ) + readme_files_dict = suc.build_readme_files_dict( repository.metadata, tool_path ) else: readme_files_dict = None repository_dependencies = metadata.get( 'repository_dependencies', None ) @@ -1515,17 +1515,19 @@ if repository_dependencies: # We need to add a root_key entry to the repository_dependencies dictionary since it will not be included in the installed tool # shed repository metadata. - root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, - repository.name, - repository.owner, - repository.installed_changeset_revision ) + root_key = container_util.generate_repository_dependencies_key_for_repository( tool_shed_repository.tool_shed, + tool_shed_repository.name, + tool_shed_repository.owner, + tool_shed_repository.installed_changeset_revision ) rd_tups_for_display = [] rd_tups = repository_dependencies[ 'repository_dependencies' ] repository_dependencies_dict_for_display[ 'root_key' ] = root_key repository_dependencies_dict_for_display[ root_key ] = rd_tups repository_dependencies_dict_for_display[ 'description' ] = repository_dependencies[ 'description' ] all_tool_dependencies = metadata.get( 'tool_dependencies', None ) - tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ) + tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans, + tool_shed_repository, + all_tool_dependencies ) valid_tools = metadata.get( 'tools', None ) workflows = metadata.get( 'workflows', None ) containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, diff -r 759d96f950b8825bcce157cdf5efbabaa0221b11 -r cfab4734097b388776035fdd2741ccf6a370b95c templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -388,7 +388,7 @@ <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a></div> %else: - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">${tool.name | h}</a> %endif %else: ${tool.name | h} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add support for installing and administering simple repository dependencies for tool shed repositories installed into a Galaxy instance.
by Bitbucket 19 Dec '12

19 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/759d96f950b8/ changeset: 759d96f950b8 user: greg date: 2012-12-19 21:57:09 summary: Add support for installing and administering simple repository dependencies for tool shed repositories installed into a Galaxy instance. affected #: 27 files diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -23,6 +23,7 @@ """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) + self.name = 'galaxy' self.new_installation = False # Read config file and check for errors self.config = config.Configuration( **kwargs ) diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3148,6 +3148,9 @@ def can_reinstall_or_activate( self ): return self.deleted @property + def has_repository_dependencies( self ): + return self.metadata and 'repository_dependencies' in self.metadata + @property def includes_tools( self ): return self.metadata and 'tools' in self.metadata @property @@ -3211,6 +3214,15 @@ uninstalled_tool_dependencies.append( tool_dependency ) return uninstalled_tool_dependencies +class RepositoryRepositoryDependencyAssociation( object ): + def __init__( self, tool_shed_repository_id=None, repository_dependency_id=None ): + self.tool_shed_repository_id = tool_shed_repository_id + self.repository_dependency_id = repository_dependency_id + +class RepositoryDependency( object ): + def __init__( self, tool_shed_repository_id=None ): + self.tool_shed_repository_id = tool_shed_repository_id + class ToolDependency( object ): installation_status = Bunch( NEVER_INSTALLED='Never installed', INSTALLING='Installing', diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -409,6 +409,19 @@ Column( "status", TrimmedString( 255 ) ), Column( "error_message", TEXT ) ) +RepositoryRepositoryDependencyAssociation.table = Table( 'repository_repository_dependency_association', metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True ), + Column( "repository_dependency_id", Integer, ForeignKey( "repository_dependency.id" ), index=True ) ) + +RepositoryDependency.table = Table( "repository_dependency", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ) ) + ToolDependency.table = Table( "tool_dependency", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -1744,7 +1757,19 @@ tool_dependencies=relation( ToolDependency, primaryjoin=( ToolShedRepository.table.c.id == ToolDependency.table.c.tool_shed_repository_id ), order_by=ToolDependency.table.c.name, - backref='tool_shed_repository' ) ) ) + backref='tool_shed_repository' ), + repository_dependencies=relation( RepositoryRepositoryDependencyAssociation, + primaryjoin=( ToolShedRepository.table.c.id == RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id ) ) ) ) + +assign_mapper( context, RepositoryRepositoryDependencyAssociation, RepositoryRepositoryDependencyAssociation.table, + properties=dict( repository=relation( ToolShedRepository, + primaryjoin=( RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id == ToolShedRepository.table.c.id ) ), + repository_dependency=relation( RepositoryDependency, + primaryjoin=( RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == RepositoryDependency.table.c.id ) ) ) ) + +assign_mapper( context, RepositoryDependency, RepositoryDependency.table, + properties=dict( repository=relation( ToolShedRepository, + primaryjoin=( RepositoryDependency.table.c.tool_shed_repository_id == ToolShedRepository.table.c.id ) ) ) ) assign_mapper( context, ToolDependency, ToolDependency.table ) diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py @@ -0,0 +1,58 @@ +""" +Migration script to add the repository_dependency and repository_repository_dependency_association tables. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +log = logging.getLogger( __name__ ) +log.setLevel( logging.DEBUG ) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) + +RepositoryDependency_table = Table( "repository_dependency", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ) ) + +RepositoryRepositoryDependencyAssociation_table = Table( "repository_repository_dependency_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True ), + Column( "repository_dependency_id", Integer, ForeignKey( "repository_dependency.id" ), index=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + RepositoryDependency_table.create() + except Exception, e: + log.debug( "Creating repository_dependency table failed: %s" % str( e ) ) + try: + RepositoryRepositoryDependencyAssociation_table.create() + except Exception, e: + log.debug( "Creating repository_repository_dependency_association table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + RepositoryRepositoryDependencyAssociation_table.drop() + except Exception, e: + log.debug( "Dropping repository_repository_dependency_association table failed: %s" % str( e ) ) + try: + RepositoryDependency_table.drop() + except Exception, e: + log.debug( "Dropping repository_dependency table failed: %s" % str( e ) ) diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -283,19 +283,19 @@ repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) - ctx_rev = shed_util.get_ctx_rev( tool_shed_url, name, self.repository_owner, installed_changeset_revision ) + ctx_rev = suc.get_ctx_rev( tool_shed_url, name, self.repository_owner, installed_changeset_revision ) print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name - tool_shed_repository = shed_util.create_or_update_tool_shed_repository( app=self.app, - name=name, - description=description, - installed_changeset_revision=installed_changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=self.app.model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=None, - owner=self.repository_owner, - dist_to_shed=True ) + tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app, + name=name, + description=description, + installed_changeset_revision=installed_changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=self.app.model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=None, + owner=self.repository_owner, + dist_to_shed=True ) shed_util.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok: diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -32,7 +32,7 @@ from cgi import FieldStorage from galaxy.util.hash_util import * from galaxy.util import listify -import galaxy.util.shed_util +import galaxy.util.shed_util_common from galaxy.web import url_for from galaxy.visualization.genome.visual_analytics import TracksterConfig @@ -890,11 +890,11 @@ def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. if self.tool_shed: - return galaxy.util.shed_util.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, - self.tool_shed, - self.repository_name, - self.repository_owner, - self.installed_changeset_revision ) + return galaxy.util.shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, + self.tool_shed, + self.repository_name, + self.repository_owner, + self.installed_changeset_revision ) return None def __get_job_run_config( self, run_configs, key, job_params=None ): # Look through runners/handlers to find one with matching parameters. diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,6 +1,9 @@ import os, tempfile, shutil, logging, urllib2 from galaxy.datatypes import checkers +from galaxy.web import url_for from galaxy import util +from galaxy.util.json import from_json_string, to_json_string +from galaxy.webapps.community.util import container_util import shed_util_common as suc from galaxy.tools.search import ToolBoxSearch from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment @@ -171,6 +174,79 @@ # Attempt to ensure we're copying an appropriate file. if is_data_index_sample_file( filename ): suc.copy_sample_file( app, filename, dest_path=dest_path ) +def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False ): + """ + Discover all repository dependencies and make sure all tool_shed_repository and associated repository_dependency records exist as well as + the dependency relationships between installed repositories. This method is called when new repositories are being installed into a Galaxy + instance and when uninstalled repositories are being reinstalled. + """ + message = '' + created_or_updated_tool_shed_repositories = [] + # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly. + filtered_repo_info_dicts = [] + # Discover all repository dependencies and retrieve information for installing them. + all_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, repo_info_dicts ) + for repo_info_dict in all_repo_info_dicts: + for name, repo_info_tuple in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) ) + relative_install_dir = os.path.join( clone_dir, name ) + # Make sure the repository was not already installed. + installed_tool_shed_repository, installed_changeset_revision = \ + repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir ) + if installed_tool_shed_repository: + if reinstalling: + if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR, + trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: + can_update = True + name = installed_tool_shed_repository.name + description = installed_tool_shed_repository.description + installed_changeset_revision = installed_tool_shed_repository.installed_changeset_revision + metadata_dict = installed_tool_shed_repository.metadata + dist_to_shed = installed_tool_shed_repository.dist_to_shed + else: + # There is a repository already installed which is a dependency of the repository being reinstalled. + can_update = False + else: + # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. + message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) + if installed_changeset_revision != changeset_revision: + message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision + else: + message += "was previously installed. " + if installed_tool_shed_repository.uninstalled: + message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " + elif installed_tool_shed_repository.deleted: + message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " + if installed_changeset_revision != changeset_revision: + message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " + message += "<b>Repository Actions</b> pop-up menu. " + if len( repo_info_dicts ) == 1: + return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message + else: + # A tool shed repository is being installed into a Galaxy instance for the first time. We may have the case where a repository + # is being reinstalled where because the repository being newly installed here may be a dependency of the repository being reinstalled. + can_update = True + installed_changeset_revision = changeset_revision + metadata_dict={} + dist_to_shed = False + if can_update: + log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name ) + tool_shed_repository = suc.create_or_update_tool_shed_repository( app=trans.app, + name=name, + description=description, + installed_changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=trans.model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=changeset_revision, + owner=repository_owner, + dist_to_shed=False ) + created_or_updated_tool_shed_repositories.append( tool_shed_repository ) + filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) + return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ): return dict( tool_shed=tool_shed, repository_name=name, @@ -179,62 +255,8 @@ tool_dicts=tool_dicts, converter_path=converter_path, display_path=display_path ) -def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, - status, current_changeset_revision=None, owner='', dist_to_shed=False ): - # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used - # to be in the Galaxy distribution, but have been moved to the main Galaxy tool shed. - if current_changeset_revision is None: - # The current_changeset_revision is not passed if a repository is being installed for the first time. If a previously installed repository - # was later uninstalled, this value should be received as the value of that change set to which the repository had been updated just prior - # to it being uninstalled. - current_changeset_revision = installed_changeset_revision - sa_session = app.model.context.current - tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url ) - if not owner: - owner = get_repository_owner_from_clone_url( repository_clone_url ) - includes_datatypes = 'datatypes' in metadata_dict - if status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED ]: - deleted = True - uninstalled = False - elif status in [ app.model.ToolShedRepository.installation_status.UNINSTALLED ]: - deleted = True - uninstalled = True - else: - deleted = False - uninstalled = False - tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, - tool_shed, - name, - owner, - installed_changeset_revision ) - if tool_shed_repository: - tool_shed_repository.description = description - tool_shed_repository.changeset_revision = current_changeset_revision - tool_shed_repository.ctx_rev = ctx_rev - tool_shed_repository.metadata = metadata_dict - tool_shed_repository.includes_datatypes = includes_datatypes - tool_shed_repository.deleted = deleted - tool_shed_repository.uninstalled = uninstalled - tool_shed_repository.status = status - else: - tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed, - name=name, - description=description, - owner=owner, - installed_changeset_revision=installed_changeset_revision, - changeset_revision=current_changeset_revision, - ctx_rev=ctx_rev, - metadata=metadata_dict, - includes_datatypes=includes_datatypes, - dist_to_shed=dist_to_shed, - deleted=deleted, - uninstalled=uninstalled, - status=status ) - sa_session.add( tool_shed_repository ) - sa_session.flush() - return tool_shed_repository def create_tool_dependency_objects( app, tool_shed_repository, relative_install_dir, set_status=True ): - # Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository. + """Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository.""" tool_dependency_objects = [] shed_config_dict = tool_shed_repository.get_shed_config_dict( app ) if shed_config_dict.get( 'tool_path' ): @@ -355,6 +377,20 @@ tool_section_dicts = generate_tool_section_dicts( tool_config=file_name, tool_sections=tool_sections ) tool_panel_dict[ guid ] = tool_section_dicts return tool_panel_dict +def generate_tool_path( repository_clone_url, changeset_revision ): + """ + Generate a tool path that guarantees repositories with the same name will always be installed + in different directories. The tool path will be of the form: + <tool shed url>/repos/<repository owner>/<repository name>/<installed changeset revision> + http://test@bx.psu.edu:9009/repos/test/filter + """ + tmp_url = suc.clean_repository_clone_url( repository_clone_url ) + # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column + items = tmp_url.split( 'repos' ) + tool_shed_url = items[ 0 ] + repo_path = items[ 1 ] + tool_shed_url = suc.clean_tool_shed_url( tool_shed_url ) + return suc.url_join( tool_shed_url, 'repos', repo_path, changeset_revision ) def generate_tool_section_dicts( tool_config=None, tool_sections=None ): tool_section_dicts = [] if tool_config is None: @@ -438,12 +474,6 @@ if converter_path and display_path: break return converter_path, display_path -def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): - url = suc.url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) - response = urllib2.urlopen( url ) - ctx_rev = response.read() - response.close() - return ctx_rev def get_headers( fname, sep, count=60, is_multi_byte=False ): """Returns a list with the first 'count' lines split by 'sep'.""" headers = [] @@ -456,6 +486,23 @@ if idx == count: break return headers +def get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ): + if all_tool_dependencies: + tool_dependencies = {} + missing_tool_dependencies = {} + for td_key, td_info_dict in all_tool_dependencies.items(): + name = td_info_dict[ 'name' ] + version = td_info_dict[ 'version' ] + type = td_info_dict[ 'type' ] + tool_dependency = get_tool_dependency_by_name_version_type_repository( trans, repository, name, version, type ) + if tool_dependency.status == trans.model.ToolDependency.installation_status.INSTALLED: + tool_dependencies[ td_key ] = td_info_dict + else: + missing_tool_dependencies[ td_key ] = td_info_dict + else: + tool_dependencies = None + missing_tool_dependencies = None + return tool_dependencies, missing_tool_dependencies def get_repository_owner( cleaned_repository_url ): items = cleaned_repository_url.split( 'repos' ) repo_path = items[ 1 ] @@ -466,6 +513,54 @@ tmp_url = suc.clean_repository_clone_url( repository_clone_url ) tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) return get_repository_owner( tmp_url ) +def get_required_repo_info_dicts( tool_shed_url, repo_info_dicts ): + """ + Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of them to the list. All + repository_dependencies entries in each of the received repo_info_dicts includes all required repositories, so only one pass through + this methid is required to retrieve all repository dependencies. + """ + if repo_info_dicts: + all_repo_info_dicts = [ rid for rid in repo_info_dicts ] + # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. + required_repository_tups = [] + for repo_info_dict in repo_info_dicts: + for repository_name, repo_info_tup in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + if repository_dependencies: + for key, val in repository_dependencies.items(): + if key in [ 'root_key', 'description' ]: + continue + toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key ) + components_list = [ toolshed, name, owner, changeset_revision ] + if components_list not in required_repository_tups: + required_repository_tups.append( components_list ) + for components_list in val: + if components_list not in required_repository_tups: + required_repository_tups.append( components_list ) + if required_repository_tups: + # The value of required_repository_tups is a list of tuples, so we need to encode it. + encoded_required_repository_tups = [] + for required_repository_tup in required_repository_tups: + encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) ) + encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups ) + encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str ) + url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_str=%s' % encoded_required_repository_str ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + required_repo_info_dict = from_json_string( text ) + required_repo_info_dicts = [] + encoded_dict_strings = required_repo_info_dict[ 'repo_info_dicts' ] + for encoded_dict_str in encoded_dict_strings: + decoded_dict = encoding_util.tool_shed_decode( encoded_dict_str ) + required_repo_info_dicts.append( decoded_dict ) + if required_repo_info_dicts: + for required_repo_info_dict in required_repo_info_dicts: + if required_repo_info_dict not in all_repo_info_dicts: + all_repo_info_dicts.append( required_repo_info_dict ) + return all_repo_info_dicts def get_tool_index_sample_files( sample_files ): """Try to return the list of all appropriate tool data sample files included in the repository.""" tool_index_sample_files = [] @@ -477,6 +572,19 @@ def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) +def get_tool_dependency_by_name_type_repository( trans, repository, name, type ): + return trans.sa_session.query( trans.model.ToolDependency ) \ + .filter( and_( trans.model.ToolDependency.table.c.tool_shed_repository_id == repository.id, + trans.model.ToolDependency.table.c.name == name, + trans.model.ToolDependency.table.c.type == type ) ) \ + .first() +def get_tool_dependency_by_name_version_type_repository( trans, repository, name, version, type ): + return trans.sa_session.query( trans.model.ToolDependency ) \ + .filter( and_( trans.model.ToolDependency.table.c.tool_shed_repository_id == repository.id, + trans.model.ToolDependency.table.c.name == name, + trans.model.ToolDependency.table.c.version == version, + trans.model.ToolDependency.table.c.type == type ) ) \ + .first() def get_tool_dependency_ids( as_string=False, **kwd ): tool_dependency_id = kwd.get( 'tool_dependency_id', None ) tool_dependency_ids = util.listify( kwd.get( 'tool_dependency_ids', None ) ) @@ -502,30 +610,6 @@ relative_install_dir = os.path.join( tool_path, partial_install_dir ) return tool_path, relative_install_dir return None, None -def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): - # This method is used only in Galaxy, not the tool shed. - sa_session = app.model.context.current - if tool_shed.find( '//' ) > 0: - tool_shed = tool_shed.split( '//' )[1] - tool_shed = tool_shed.rstrip( '/' ) - return sa_session.query( app.model.ToolShedRepository ) \ - .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed, - app.model.ToolShedRepository.table.c.name == name, - app.model.ToolShedRepository.table.c.owner == owner, - app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ - .first() -def get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, installed_changeset_revision ): - # This method is used only in Galaxy, not the tool shed. - sa_session = app.model.context.current - if tool_shed.find( '//' ) > 0: - tool_shed = tool_shed.split( '//' )[1] - tool_shed = tool_shed.rstrip( '/' ) - return sa_session.query( app.model.ToolShedRepository ) \ - .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed, - app.model.ToolShedRepository.table.c.name == name, - app.model.ToolShedRepository.table.c.owner == owner, - app.model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision ) ) \ - .first() def get_tool_version( app, tool_id ): sa_session = app.model.context.current return sa_session.query( app.model.ToolVersion ) \ @@ -908,6 +992,35 @@ trans.sa_session.add( tool_dependency ) trans.sa_session.flush() return removed, error_message +def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple, clone_dir ): + """ + Handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated + in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one + that was previously installed. We'll look in the database instead of on disk since the repository may be uninstalled. + """ + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url ) + # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset + # revision to see if it was previously installed using one of them. + url = suc.url_join( tool_shed_url, + 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ + ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + #clone_path, clone_directory = os.path.split( clone_dir ) + changeset_revisions = util.listify( text ) + for previous_changeset_revision in changeset_revisions: + tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, + tool_shed, + repository_name, + repository_owner, + previous_changeset_revision ) + if tool_shed_repository and tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]: + return tool_shed_repository, previous_changeset_revision + return None, None def update_tool_shed_repository_status( app, tool_shed_repository, status ): sa_session = app.model.context.current tool_shed_repository.status = status diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -57,26 +57,24 @@ requirements_dict[ 'install_dir' ] = install_dir tool_dependencies[ dependency_key ] = requirements_dict return tool_dependencies -def build_readme_files_dict( repository_metadata ): +def build_readme_files_dict( metadata ): """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received repository_metadata.""" readme_files_dict = {} - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'readme_files' in metadata: - for relative_path_to_readme_file in metadata[ 'readme_files' ]: - readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ] - full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file ) - try: - f = open( full_path_to_readme_file, 'r' ) - text = f.read() - f.close() - readme_files_dict[ readme_file_name ] = translate_string( text, to_html=False ) - except Exception, e: - log.debug( "Error reading README file '%s' defined in metadata for repository '%s', revision '%s': %s" % \ - ( str( relative_path_to_readme_file ), str( repository_name ), str( changeset_revision ), str( e ) ) ) + if metadata and 'readme_files' in metadata: + for relative_path_to_readme_file in metadata[ 'readme_files' ]: + readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ] + full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file ) + try: + f = open( full_path_to_readme_file, 'r' ) + text = f.read() + f.close() + readme_files_dict[ readme_file_name ] = translate_string( text, to_html=False ) + except Exception, e: + log.debug( "Error reading README file '%s' defined in metadata: %s" % ( str( relative_path_to_readme_file ), str( e ) ) ) return readme_files_dict -def build_repository_containers_for_galaxy( trans, toolshed_base_url, repository_name, repository_owner, changeset_revision, - readme_files_dict, repository_dependencies, tool_dependencies ): +def build_repository_containers_for_galaxy( trans, toolshed_base_url, repository_name, repository_owner, changeset_revision, repository, datatypes, + invalid_tools, missing_tool_dependencies, readme_files_dict, repository_dependencies, tool_dependencies, + valid_tools, workflows ): """Return a dictionary of containers for the received repository's dependencies and readme files for display during installation to Galaxy.""" containers_dict = dict( readme_files=None, repository_dependencies=None, tool_dependencies=None ) if readme_files_dict or repository_dependencies or tool_dependencies: @@ -91,9 +89,23 @@ tool_dependencies ) try: folder_id = 0 + # Datatypes container. + if datatypes: + folder_id, datatypes_root_folder = container_util.build_datatypes_folder( folder_id, datatypes ) + containers_dict[ 'datatypes' ] = datatypes_root_folder + # Invalid tools container. + if invalid_tools: + folder_id, invalid_tools_root_folder = container_util.build_invalid_tools_folder( folder_id, + invalid_tools, + changeset_revision, + repository=repository, + label='Invalid tools' ) + containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder + # Readme files container. if readme_files_dict: folder_id, readme_files_root_folder = build_readme_files_folder( folder_id, readme_files_dict ) containers_dict[ 'readme_files' ] = readme_files_root_folder + # Repository dependencies container. if repository_dependencies: folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, repository_name=repository_name, @@ -102,9 +114,28 @@ folder_id=folder_id, repository_dependencies=repository_dependencies ) containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + # Tool dependencies container. if tool_dependencies: folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + # Missing tool dependencies container. + if missing_tool_dependencies: + folder_id, missing_tool_dependencies_root_folder = \ + container_util.build_tool_dependencies_folder( folder_id, missing_tool_dependencies, label='Missing tool dependencies', for_galaxy=True ) + containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder + # Valid tools container. + if valid_tools: + folder_id, valid_tools_root_folder = container_util.build_tools_folder( folder_id, + valid_tools, + repository, + changeset_revision, + label='Valid tools', + description='click the name to inspect the tool metadata' ) + containers_dict[ 'valid_tools' ] = valid_tools_root_folder + # Workflows container. + if workflows: + folder_id, workflows_root_folder = container_util.build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) + containers_dict[ 'workflows' ] = workflows_root_folder except Exception, e: log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) ) finally: @@ -140,9 +171,10 @@ label='Invalid tools' ) containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder # Readme files container. - readme_files_dict = build_readme_files_dict( repository_metadata ) - folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) - containers_dict[ 'readme_files' ] = readme_files_root_folder + if metadata and 'readme_files' in metadata: + readme_files_dict = build_readme_files_dict( metadata ) + folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) + containers_dict[ 'readme_files' ] = readme_files_root_folder # Repository dependencies container. toolshed_base_url = str( url_for( '/', qualified=True ) ).rstrip( '/' ) folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, @@ -177,6 +209,64 @@ finally: lock.release() return containers_dict +def build_repository_dependency_relationships( trans, repo_info_dicts, tool_shed_repositories ): + """ + Build relationships between installed tool shed repositories and other installed tool shed repositories upon which they depend. These + relationships are defined in the repository_dependencies entry for each dictionary in the received list of repo_info_dicts. Each of + these dictionaries is associated with a repository in the received tool_shed_repositories list. + """ + for repo_info_dict in repo_info_dicts: + for name, repo_info_tuple in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + get_repo_info_tuple_contents( repo_info_tuple ) + if repository_dependencies: + for key, val in repository_dependencies.items(): + if key in [ 'root_key', 'description' ]: + continue + dependent_repository = None + dependent_toolshed, dependent_name, dependent_owner, dependent_changeset_revision = container_util.get_components_from_key( key ) + for tsr in tool_shed_repositories: + # Get the the tool_shed_repository defined by name, owner and changeset_revision. This is the repository that will be + # dependent upon each of the tool shed repositories contained in val. + # TODO: Check tool_shed_repository.tool_shed as well when repository dependencies across tool sheds is supported. + if tsr.name == dependent_name and tsr.owner == dependent_owner and tsr.changeset_revision == dependent_changeset_revision: + dependent_repository = tsr + break + if dependent_repository is None: + # The dependent repository is not in the received list so look in the database. + dependent_repository = get_or_create_tool_shed_repository( trans, dependent_toolshed, dependent_name, dependent_owner, dependent_changeset_revision ) + # Process each repository_dependency defined for the current dependent repository. + for repository_dependency_components_list in val: + required_repository = None + rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency_components_list + # Get the the tool_shed_repository defined by rd_name, rd_owner and rd_changeset_revision. This is the repository that will be + # required by the current dependent_repository. + # TODO: Check tool_shed_repository.tool_shed as well when repository dependencies across tool sheds is supported. + for tsr in tool_shed_repositories: + if tsr.name == rd_name and tsr.owner == rd_owner and tsr.changeset_revision == rd_changeset_revision: + required_repository = tsr + break + if required_repository is None: + # The required repository is not in the received list so look in the database. + required_repository = get_or_create_tool_shed_repository( trans, rd_toolshed, rd_name, rd_owner, rd_changeset_revision ) + # Ensure there is a repository_dependency relationship between dependent_repository and required_repository. + rrda = None + for rd in dependent_repository.repository_dependencies: + if rd.repository_dependency.tool_shed_repository_id == required_repository.id: + rrda = rd + break + if not rrda: + # Make sure required_repository is in the repository_dependency table. + repository_dependency = get_repository_dependency_by_repository_id( trans, required_repository.id ) + if not repository_dependency: + repository_dependency = trans.model.RepositoryDependency( tool_shed_repository_id=required_repository.id ) + trans.sa_session.add( repository_dependency ) + trans.sa_session.flush() + # Build the relationship between the dependent_repository and the required_repository. + rrda = trans.model.RepositoryRepositoryDependencyAssociation( tool_shed_repository_id=dependent_repository.id, + repository_dependency_id=repository_dependency.id ) + trans.sa_session.add( rrda ) + trans.sa_session.flush() def build_repository_ids_select_field( trans, cntrller, name='repository_ids', multiple=True, display='checkboxes' ): """Method called from both Galaxy and the Tool Shed to generate the current list of repositories for resetting metadata.""" repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) @@ -546,6 +636,60 @@ trans.sa_session.add( repository_metadata ) trans.sa_session.flush() return repository_metadata +def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, + status, current_changeset_revision=None, owner='', dist_to_shed=False ): + # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used + # to be in the Galaxy distribution, but have been moved to the main Galaxy tool shed. + if current_changeset_revision is None: + # The current_changeset_revision is not passed if a repository is being installed for the first time. If a previously installed repository + # was later uninstalled, this value should be received as the value of that change set to which the repository had been updated just prior + # to it being uninstalled. + current_changeset_revision = installed_changeset_revision + sa_session = app.model.context.current + tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) + if not owner: + owner = get_repository_owner_from_clone_url( repository_clone_url ) + includes_datatypes = 'datatypes' in metadata_dict + if status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED ]: + deleted = True + uninstalled = False + elif status in [ app.model.ToolShedRepository.installation_status.UNINSTALLED ]: + deleted = True + uninstalled = True + else: + deleted = False + uninstalled = False + tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, + tool_shed, + name, + owner, + installed_changeset_revision ) + if tool_shed_repository: + tool_shed_repository.description = description + tool_shed_repository.changeset_revision = current_changeset_revision + tool_shed_repository.ctx_rev = ctx_rev + tool_shed_repository.metadata = metadata_dict + tool_shed_repository.includes_datatypes = includes_datatypes + tool_shed_repository.deleted = deleted + tool_shed_repository.uninstalled = uninstalled + tool_shed_repository.status = status + else: + tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed, + name=name, + description=description, + owner=owner, + installed_changeset_revision=installed_changeset_revision, + changeset_revision=current_changeset_revision, + ctx_rev=ctx_rev, + metadata=metadata_dict, + includes_datatypes=includes_datatypes, + dist_to_shed=dist_to_shed, + deleted=deleted, + uninstalled=uninstalled, + status=status ) + sa_session.add( tool_shed_repository ) + sa_session.flush() + return tool_shed_repository def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, repository=None, repository_metadata=None, metadata=None, repository_dependencies=None ): """ @@ -585,6 +729,20 @@ repository_dependencies, metadata.get( 'tool_dependencies', None ) ) return repo_info_dict +def ensure_required_repositories_exist_for_reinstall( trans, repository_dependencies ): + """ + Inspect the received repository_dependencies dictionary and make sure tool_shed_repository objects exist in the database for each entry. These + tool_shed_repositories do not necessarily have to exist on disk, and if they do not, their status will be marked appropriately. They must exist + in the database in order for repository dependency relationships to be properly built. + """ + for key, val in repository_dependencies.items(): + if key in [ 'root_key', 'description' ]: + continue + tool_shed, name, owner, changeset_revision = container_util.get_components_from_key( key ) + repository = get_or_create_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ) + for repository_components_list in val: + tool_shed, name, owner, changeset_revision = repository_components_list + repository = get_or_create_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ) def generate_clone_url_for_installed_repository( app, repository ): """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" tool_shed_url = get_url_from_repository_tool_shed( app, repository ) @@ -765,9 +923,18 @@ # See if we have a repository dependencies defined. if name == 'repository_dependencies.xml': path_to_repository_dependencies_config = os.path.join( root, name ) - metadata_dict, error_message = generate_repository_dependency_metadata( app, path_to_repository_dependencies_config, metadata_dict ) - if error_message: - invalid_file_tups.append( ( name, error_message ) ) + if app.name == 'community': + metadata_dict, error_message = generate_repository_dependency_metadata_for_tool_shed( app, + path_to_repository_dependencies_config, + metadata_dict ) + if error_message: + invalid_file_tups.append( ( name, error_message ) ) + elif app.name == 'galaxy': + metadata_dict, error_message = generate_repository_dependency_metadata_for_installed_repository( app, + path_to_repository_dependencies_config, + metadata_dict ) + if error_message: + invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = get_relative_path_to_repository_file( root, @@ -860,8 +1027,42 @@ if requirements_dict: tool_dependencies_dict[ dependency_key ] = requirements_dict return tool_dependencies_dict -def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict ): - """Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config.""" +def generate_repository_dependency_metadata_for_installed_repository( app, repository_dependencies_config, metadata_dict ): + """ + Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method + is called only from Galaxy. + """ + repository_dependencies_tups = [] + error_message = '' + try: + # Make sure we're looking at a valid repository_dependencies.xml file. + tree = util.parse_xml( repository_dependencies_config ) + root = tree.getroot() + is_valid = root.tag == 'repositories' + except Exception, e: + error_message = "Error parsing %s, exception: %s" % ( repository_dependencies_config, str( e ) ) + log.debug( error_message ) + is_valid = False + if is_valid: + sa_session = app.model.context.current + for repository_elem in root.findall( 'repository' ): + toolshed = repository_elem.attrib[ 'toolshed' ] + name = repository_elem.attrib[ 'name' ] + owner = repository_elem.attrib[ 'owner'] + changeset_revision = repository_elem.attrib[ 'changeset_revision' ] + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in repository_dependencies_tups: + repository_dependencies_tups.append( repository_dependencies_tup ) + if repository_dependencies_tups: + repository_dependencies_dict = dict( description=root.get( 'description' ), + repository_dependencies=repository_dependencies_tups ) + metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict + return metadata_dict, error_message +def generate_repository_dependency_metadata_for_tool_shed( app, repository_dependencies_config, metadata_dict ): + """ + Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method + is called only from the tool shed. + """ repository_dependencies_tups = [] error_message = '' try: @@ -1111,6 +1312,12 @@ # quiet = True _ui.setconfig( 'ui', 'quiet', True ) return _ui +def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): + url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) + response = urllib2.urlopen( url ) + ctx_rev = response.read() + response.close() + return ctx_rev def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ): """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision.""" stripped_filename = strip_path( filename ) @@ -1223,6 +1430,25 @@ # We've found the changeset in the changelog for which we need to get the next downloadable changset. found_after_changeset_revision = True return None +def get_or_create_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ): + repository = get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision ) + if not repository: + tool_shed_url = get_url_from_tool_shed( trans.app, tool_shed ) + repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) + ctx_rev = get_ctx_rev( tool_shed_url, name, owner, installed_changeset_revision ) + print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name + repository = create_or_update_tool_shed_repository( app=self.app, + name=name, + description=None, + installed_changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=self.app.model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=None, + owner=sowner, + dist_to_shed=False ) + return repository def get_ordered_downloadable_changeset_revisions( repository, repo ): """Return an ordered list of changeset_revisions defined by a repository changelog.""" changeset_tups = [] @@ -1366,6 +1592,23 @@ repository_dependency[ 1 ], repository_dependency[ 2 ], repository_dependency[ 3] ) +def get_repository_dependency_by_repository_id( trans, decoded_repository_id ): + return trans.sa_session.query( trans.model.RepositoryDependency ) \ + .filter( trans.model.RepositoryDependency.table.c.tool_shed_repository_id == decoded_repository_id ) \ + .first() +def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ): + repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app=app, + tool_shed=tool_shed, + name=name, + owner=owner, + installed_changeset_revision=changeset_revision ) + if not repository: + repository = get_tool_shed_repository_by_shed_name_owner_changeset_revision( app=app, + tool_shed=tool_shed, + name=name, + owner=owner, + changeset_revision=changeset_revision ) + return repository def get_repository_file_contents( file_path ): if checkers.is_gzip( file_path ): safe_str = to_safe_string( '\ngzip compressed file\n' ) @@ -1512,6 +1755,30 @@ tool_path = shed_config_dict[ 'tool_path' ] relative_install_dir = partial_install_dir return shed_tool_conf, tool_path, relative_install_dir +def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): + # This method is used only in Galaxy, not the tool shed. + sa_session = app.model.context.current + if tool_shed.find( '//' ) > 0: + tool_shed = tool_shed.split( '//' )[1] + tool_shed = tool_shed.rstrip( '/' ) + return sa_session.query( app.model.ToolShedRepository ) \ + .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed, + app.model.ToolShedRepository.table.c.name == name, + app.model.ToolShedRepository.table.c.owner == owner, + app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ + .first() +def get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, installed_changeset_revision ): + # This method is used only in Galaxy, not the tool shed. + sa_session = app.model.context.current + if tool_shed.find( '//' ) > 0: + tool_shed = tool_shed.split( '//' )[1] + tool_shed = tool_shed.rstrip( '/' ) + return sa_session.query( app.model.ToolShedRepository ) \ + .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed, + app.model.ToolShedRepository.table.c.name == name, + app.model.ToolShedRepository.table.c.owner == owner, + app.model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision ) ) \ + .first() def get_tool_shed_from_clone_url( repository_clone_url ): tmp_url = clean_repository_clone_url( repository_clone_url ) return tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) @@ -1557,6 +1824,16 @@ return shed_url # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. return None +def get_url_from_tool_shed( app, tool_shed ): + # The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: + # http://toolshed.g2.bx.psu.edu/ + for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): + if shed_url.find( tool_shed ) >= 0: + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + return shed_url + # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. + return None def get_user_by_username( trans, username ): """Get a user from the database by username""" return trans.sa_session.query( trans.model.User ) \ diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -12,6 +12,7 @@ """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) + self.name = "community" # Read config file and check for errors self.config = config.Configuration( **kwargs ) self.config.check() diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1338,7 +1338,7 @@ changeset_revision = kwd[ 'changeset_revision' ] repository = suc.get_repository_by_name_and_owner( trans, repository_name, repository_owner ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) - return suc.build_readme_files_dict( repository_metadata ) + return suc.build_readme_files_dict( repository_metadata.metadata ) @web.json def get_repository_dependencies( self, trans, **kwd ): """Return an encoded dictionary of all repositories upon which the contents of the received repository depends.""" diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -218,7 +218,7 @@ else: repository_dependencies_root_folder = None return folder_id, repository_dependencies_root_folder -def build_tools_folder( folder_id, tool_dicts, repository, changeset_revision, valid=True, label='Valid tools' ): +def build_tools_folder( folder_id, tool_dicts, repository, changeset_revision, valid=True, label='Valid tools', description=None ): """Return a folder hierarchy containing valid tools.""" if tool_dicts: tool_id = 0 @@ -226,6 +226,8 @@ tools_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 folder = Folder( id=folder_id, key='tools', label=label, parent=tools_root_folder ) + if description: + folder.description = description tools_root_folder.folders.append( folder ) # Insert a header row. tool_id += 1 @@ -239,6 +241,10 @@ repository_id='', changeset_revision='' ) folder.valid_tools.append( tool ) + if repository: + repository_id = repository.id + else: + repository_id = '' for tool_dict in tool_dicts: tool_id += 1 if 'requirements' in tool_dict: @@ -256,7 +262,7 @@ description=tool_dict[ 'description' ], version=tool_dict[ 'version' ], requirements=requirements_str, - repository_id=repository.id, + repository_id=repository_id, changeset_revision=changeset_revision ) folder.valid_tools.append( tool ) else: diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/webapps/demo_sequencer/app.py --- a/lib/galaxy/webapps/demo_sequencer/app.py +++ b/lib/galaxy/webapps/demo_sequencer/app.py @@ -6,6 +6,7 @@ """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) + self.name = "demo_sequencer" # Read config file and check for errors self.config = config.Configuration( **kwargs ) self.config.check() diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/webapps/demo_sequencer/buildapp.py --- a/lib/galaxy/webapps/demo_sequencer/buildapp.py +++ b/lib/galaxy/webapps/demo_sequencer/buildapp.py @@ -55,7 +55,7 @@ sys.exit( 1 ) atexit.register( app.shutdown ) # Create the universe WSGI application - webapp = galaxy.webapps.demo_sequencer.framework.WebApplication( app, session_cookie='galaxydemo_sequencersession' ) + webapp = galaxy.webapps.demo_sequencer.framework.WebApplication( app, session_cookie='galaxydemo_sequencersession', name="demo_sequencer" ) add_ui_controllers( webapp, app ) # These two routes handle our simple needs at the moment webapp.add_route( '/:controller/:action', action='index' ) diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -547,20 +547,6 @@ galaxy_url = url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) - def generate_tool_path( self, repository_clone_url, changeset_revision ): - """ - Generate a tool path that guarantees repositories with the same name will always be installed - in different directories. The tool path will be of the form: - <tool shed url>/repos/<repository owner>/<repository name>/<installed changeset revision> - http://test@bx.psu.edu:9009/repos/test/filter - """ - tmp_url = suc.clean_repository_clone_url( repository_clone_url ) - # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column - items = tmp_url.split( 'repos' ) - tool_shed_url = items[ 0 ] - repo_path = items[ 1 ] - tool_shed_url = suc.clean_tool_shed_url( tool_shed_url ) - return suc.url_join( tool_shed_url, 'repos', repo_path, changeset_revision ) @web.json @web.require_admin def get_file_contents( self, trans, file_path ): @@ -585,59 +571,11 @@ raw_text = response.read() response.close() if len( raw_text ) > 2: - text = json.from_json_string( encoding_util.tool_shed_decode( raw_text ) ) - log.debug( text ) + encoded_text = from_json_string( raw_text ) + text = encoding_util.tool_shed_decode( encoded_text ) else: text = '' return text - def get_required_repo_info_dicts( self, tool_shed_url, repo_info_dicts ): - """ - Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of them to the list. All - repository_dependencies entries in each of the received repo_info_dicts includes all required repositories, so only one pass through - this methid is required to retrieve all repository dependencies. - """ - if repo_info_dicts: - all_repo_info_dicts = [ rid for rid in repo_info_dicts ] - # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. - required_repository_tups = [] - for repo_info_dict in repo_info_dicts: - for repository_name, repo_info_tup in repo_info_dict.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - if repository_dependencies: - for key, val in repository_dependencies.items(): - if key in [ 'root_key', 'description' ]: - continue - toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key ) - components_list = [ toolshed, name, owner, changeset_revision ] - if components_list not in required_repository_tups: - required_repository_tups.append( components_list ) - for components_list in val: - if components_list not in required_repository_tups: - required_repository_tups.append( components_list ) - if required_repository_tups: - # The value of required_repository_tups is a list of tuples, so we need to encode it. - encoded_required_repository_tups = [] - for required_repository_tup in required_repository_tups: - encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) ) - encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups ) - encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str ) - url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_str=%s' % encoded_required_repository_str ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() - if text: - required_repo_info_dict = from_json_string( text ) - required_repo_info_dicts = [] - encoded_dict_strings = required_repo_info_dict[ 'repo_info_dicts' ] - for encoded_dict_str in encoded_dict_strings: - decoded_dict = encoding_util.tool_shed_decode( encoded_dict_str ) - required_repo_info_dicts.append( decoded_dict ) - if required_repo_info_dicts: - for required_repo_info_dict in required_repo_info_dicts: - if required_repo_info_dict not in all_repo_info_dicts: - all_repo_info_dicts.append( required_repo_info_dict ) - return all_repo_info_dicts def get_versions_of_tool( self, app, guid ): tool_version = shed_util.get_tool_version( app, guid ) return tool_version.get_version_ids( app, reverse=True ) @@ -748,7 +686,7 @@ shed_util.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING ) repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple - relative_clone_dir = self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) + relative_clone_dir = shed_util.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) clone_dir = os.path.join( tool_path, relative_clone_dir ) relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name ) install_dir = os.path.join( tool_path, relative_install_dir ) @@ -908,13 +846,13 @@ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) if not repository: return trans.show_error_message( 'Invalid repository specified.' ) + tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', **kwd ) ) if repository.can_install and operation == 'install': # Send a request to the tool shed to install the repository. - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) url = suc.url_join( tool_shed_url, 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision, ( url_for( '/', qualified=True ) ) ) ) @@ -939,10 +877,50 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message = "The repository information has been updated." + metadata = repository.metadata + datatypes = metadata.get( 'datatypes', None ) + invalid_tools = metadata.get( 'invalid_tools', None ) + if repository.has_readme_files: + readme_files_dict = suc.build_readme_files_dict( repository.metadata ) + else: + readme_files_dict = None + repository_dependencies = metadata.get( 'repository_dependencies', None ) + repository_dependencies_dict_for_display = {} + if repository_dependencies: + # We need to add a root_key entry to the repository_dependencies dictionary since it will not be included in the installed tool + # shed repository metadata. + root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, + repository.name, + repository.owner, + repository.installed_changeset_revision ) + rd_tups_for_display = [] + rd_tups = repository_dependencies[ 'repository_dependencies' ] + repository_dependencies_dict_for_display[ 'root_key' ] = root_key + repository_dependencies_dict_for_display[ root_key ] = rd_tups + repository_dependencies_dict_for_display[ 'description' ] = repository_dependencies[ 'description' ] + all_tool_dependencies = metadata.get( 'tool_dependencies', None ) + tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ) + valid_tools = metadata.get( 'tools', None ) + workflows = metadata.get( 'workflows', None ) + containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, + toolshed_base_url=tool_shed_url, + repository_name=repository.name, + repository_owner=repository.owner, + changeset_revision=repository.installed_changeset_revision, + repository=repository, + datatypes=datatypes, + invalid_tools=invalid_tools, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=repository_dependencies_dict_for_display, + tool_dependencies=tool_dependencies, + valid_tools=valid_tools, + workflows=workflows ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, repo_files_dir=repo_files_dir, + containers_dict=containers_dict, message=message, status=status ) @web.expose @@ -1153,8 +1131,8 @@ shed_tool_conf = kwd[ 'shed_tool_conf' ] else: install_tool_dependencies = False - # If installing a repository that includes no tools, get the relative tool_path from the file to which the - # migrated_tools_config setting points. + # If installing a repository that includes no tools, get the relative tool_path from the file to which the migrated_tools_config + # setting points. shed_tool_conf = trans.app.config.migrated_tools_config # Get the tool path by searching the list of shed_tool_confs for the dictionary that contains the information about shed_tool_conf. for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: @@ -1167,61 +1145,20 @@ if file_name == shed_tool_conf: tool_path = shed_tool_conf_dict[ 'tool_path' ] break - # Make sure all tool_shed_repository records exist. - created_or_updated_tool_shed_repositories = [] - # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly. - filtered_repo_info_dicts = [] - # Disciver all repository dependencies and retrieve information for installing them. - repo_info_dicts = self.get_required_repo_info_dicts( tool_shed_url, repo_info_dicts ) - for repo_info_dict in repo_info_dicts: - for name, repo_info_tuple in repo_info_dict.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) - clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) ) - relative_install_dir = os.path.join( clone_dir, name ) - # Make sure the repository was not already installed. - installed_tool_shed_repository, installed_changeset_revision = self.repository_was_previously_installed( trans, - tool_shed_url, - name, - repo_info_tuple, - clone_dir ) - if installed_tool_shed_repository: - message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) - if installed_changeset_revision != changeset_revision: - message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision - else: - message += "was previously installed. " - if installed_tool_shed_repository.uninstalled: - message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " - elif installed_tool_shed_repository.deleted: - message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " - if installed_changeset_revision != changeset_revision: - message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " - message += "<b>Repository Actions</b> pop-up menu. " - message+= 'Click <a href="%s">here</a> to manage the repository. ' % \ - ( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) ) - status = 'error' - if len( repo_info_dicts ) == 1: - new_kwd = dict( message=message, status=status ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='browse_repositories', - **new_kwd ) ) - else: - log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name ) - tool_shed_repository = shed_util.create_or_update_tool_shed_repository( app=trans.app, - name=name, - description=description, - installed_changeset_revision=changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=trans.model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=changeset_revision, - owner=repository_owner, - dist_to_shed=False ) - created_or_updated_tool_shed_repositories.append( tool_shed_repository ) - filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) + created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ + shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False ) + if message and len( repo_info_dicts ) == 1: + message+= 'Click <a href="%s">here</a> to manage the repository. ' % \ + ( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + message=message, + status='error' ) ) if created_or_updated_tool_shed_repositories: + if install_repository_dependencies: + # Build repository dependency relationships. + suc.build_repository_dependency_relationships( trans, repo_info_dicts, created_or_updated_tool_shed_repositories ) + # Handle contained tools. if includes_tools and ( new_tool_panel_section or tool_panel_section ): if new_tool_panel_section: section_id = new_tool_panel_section.lower().replace( ' ', '_' ) @@ -1286,11 +1223,8 @@ repo_info_dict = repo_info_dicts[ 0 ] name = repo_info_dict.keys()[ 0 ] repo_info_tuple = repo_info_dict[ name ] - if len( repo_info_tuple ) == 6: - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple - repository_dependencies = None - elif len( repo_info_tuple ) == 7: - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) url = suc.url_join( tool_shed_url, 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \ ( name, repository_owner, changeset_revision ) ) @@ -1303,9 +1237,15 @@ repository_name=name, repository_owner=repository_owner, changeset_revision=changeset_revision, + repository=None, + datatypes=None, + invalid_tools=None, + missing_tool_dependencies=None, readme_files_dict=readme_files_dict, repository_dependencies=repository_dependencies, - tool_dependencies=tool_dependencies ) + tool_dependencies=tool_dependencies, + valid_tools=None, + workflows=None ) else: containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None ) # Handle tool dependencies chack box. @@ -1338,18 +1278,23 @@ @web.expose @web.require_admin def reinstall_repository( self, trans, **kwd ): + """ + Reinstall a tool shed repository that has been previously uninstalled, making sure to handle all repository and tool dependencies of the + repository. + """ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) no_changes = kwd.get( 'no_changes', '' ) no_changes_checked = CheckboxField.is_checked( no_changes ) + install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section = kwd.get( 'tool_panel_section', '' ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) - clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) + clone_dir = os.path.join( tool_path, shed_util.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) tool_section = None @@ -1406,28 +1351,34 @@ else: tool_section = None # The repository's status must be updated from 'Uninstall' to 'New' when initiating reinstall so the repository_installation_updater will function. - tool_shed_repository = shed_util.create_or_update_tool_shed_repository( trans.app, - tool_shed_repository.name, - tool_shed_repository.description, - tool_shed_repository.installed_changeset_revision, - tool_shed_repository.ctx_rev, - repository_clone_url, - tool_shed_repository.metadata, - trans.model.ToolShedRepository.installation_status.NEW, - tool_shed_repository.installed_changeset_revision, - tool_shed_repository.owner, - tool_shed_repository.dist_to_shed ) - ctx_rev = shed_util.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) + tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app, + tool_shed_repository.name, + tool_shed_repository.description, + tool_shed_repository.installed_changeset_revision, + tool_shed_repository.ctx_rev, + repository_clone_url, + tool_shed_repository.metadata, + trans.model.ToolShedRepository.installation_status.NEW, + tool_shed_repository.installed_changeset_revision, + tool_shed_repository.owner, + tool_shed_repository.dist_to_shed ) + ctx_rev = suc.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) + repo_info_dicts = [] repo_info_dict = kwd.get( 'repo_info_dict', None ) - # The repo_info_dict should be encoded. - if not repo_info_dict: + if repo_info_dict: + # The repo_info_dict should be encoded. + repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) + else: # Entering this if block used to happen only if the tool_shed_repository does not include any valid tools. After repository dependencies - # were introduced, it may never happen, but will keep the block just in case. - repository_dependencies = self.get_repository_dependencies( trans=trans, - repository_id=repository_id, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - changeset_revision=tool_shed_repository.installed_changeset_revision ) + # were introduced, it may never happen, but we'll keep the block just in case. + if install_repository_dependencies: + repository_dependencies = self.get_repository_dependencies( trans=trans, + repository_id=repository_id, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + changeset_revision=tool_shed_repository.installed_changeset_revision ) + else: + repository_dependencies = None repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) ) repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, @@ -1440,6 +1391,16 @@ metadata=metadata, repository_dependencies=repository_dependencies ) repo_info_dict = encoding_util.tool_shed_encode( repo_info_dict ) + repo_info_dicts.append( repo_info_dict ) + # Make sure all tool_shed_repository records exist. + created_or_updated_tool_shed_repositories = [ tool_shed_repository ] + if install_repository_dependencies: + created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts = \ + shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=True ) + if len( created_or_updated_tool_shed_repositories ) > 1: + # Build repository dependency relationships. + suc.build_repository_dependency_relationships( trans, filtered_repo_info_dicts, created_or_updated_tool_shed_repositories ) + encoded_repository_ids = [ trans.security.encode_id( r.id ) for r in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, install_tool_dependencies=install_tool_dependencies, @@ -1451,12 +1412,12 @@ tool_panel_section=tool_panel_section, tool_path=tool_path, tool_panel_section_key=tool_panel_section_key, - tool_shed_repository_ids=[ repository_id ], + tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='initiate_repository_installation', - shed_repository_ids=repository_id, + shed_repository_ids=encoded_repository_ids, encoded_kwd=encoded_kwd, reinstalling=True ) ) @web.json @@ -1481,48 +1442,23 @@ return rval @web.expose @web.require_admin - def repository_was_previously_installed( self, trans, tool_shed_url, repository_name, repo_info_tuple, clone_dir ): - # Handle case where the repository was previously installed using an older changeset_revsion, but later the repository was updated - # in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one - # that was previously installed. We'll look in the database instead of on disk since the repository may be uninstalled. - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) - tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url ) - # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset - # revision to see if it was previously installed using one of them. - url = suc.url_join( tool_shed_url, - 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ - ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() - if text: - #clone_path, clone_directory = os.path.split( clone_dir ) - changeset_revisions = util.listify( text ) - for previous_changeset_revision in changeset_revisions: - tool_shed_repository = shed_util.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, - tool_shed, - repository_name, - repository_owner, - previous_changeset_revision ) - if tool_shed_repository and tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]: - return tool_shed_repository, previous_changeset_revision - return None, None - @web.expose - @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) metadata = tool_shed_repository.metadata tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) - ctx_rev = shed_util.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) + ctx_rev = suc.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) repository_dependencies = self.get_repository_dependencies( trans=trans, repository_id=repository_id, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, changeset_revision=tool_shed_repository.installed_changeset_revision ) + if repository_dependencies: + includes_repository_dependencies = True + else: + includes_repository_dependencies = False repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.installed_changeset_revision, @@ -1561,24 +1497,51 @@ message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' - if metadata and 'readme_files' in metadata: - url = suc.url_join( tool_shed_url, - 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \ - ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) ) - response = urllib2.urlopen( url ) - raw_text = response.read() - response.close() - readme_files_dict = from_json_string( raw_text ) - tool_dependencies = metadata.get( 'tool_dependencies', None ) + if metadata: + datatypes = metadata.get( 'datatypes', None ) + invalid_tools = metadata.get( 'invalid_tools', None ) + if tool_shed_repository.has_readme_files: + url = suc.url_join( tool_shed_url, + 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \ + ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) ) + response = urllib2.urlopen( url ) + raw_text = response.read() + response.close() + readme_files_dict = from_json_string( raw_text ) + else: + readme_files_dict = None repository_dependencies = metadata.get( 'repository_dependencies', None ) + repository_dependencies_dict_for_display = {} + if repository_dependencies: + # We need to add a root_key entry to the repository_dependencies dictionary since it will not be included in the installed tool + # shed repository metadata. + root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, + repository.name, + repository.owner, + repository.installed_changeset_revision ) + rd_tups_for_display = [] + rd_tups = repository_dependencies[ 'repository_dependencies' ] + repository_dependencies_dict_for_display[ 'root_key' ] = root_key + repository_dependencies_dict_for_display[ root_key ] = rd_tups + repository_dependencies_dict_for_display[ 'description' ] = repository_dependencies[ 'description' ] + all_tool_dependencies = metadata.get( 'tool_dependencies', None ) + tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ) + valid_tools = metadata.get( 'tools', None ) + workflows = metadata.get( 'workflows', None ) containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, changeset_revision=tool_shed_repository.installed_changeset_revision, + repository=tool_shed_repository, + datatypes=datatypes, + invalid_tools=invalid_tools, + missing_tool_dependencies=missing_tool_dependencies, readme_files_dict=readme_files_dict, repository_dependencies=repository_dependencies, - tool_dependencies=tool_dependencies ) + tool_dependencies=tool_dependencies, + valid_tools=valid_tools, + workflows=workflows ) else: containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None ) # Handle repository dependencies check box. @@ -1597,6 +1560,8 @@ repository=tool_shed_repository, no_changes_check_box=no_changes_check_box, original_section_name=original_section_name, + includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, + includes_repository_dependencies=includes_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, install_tool_dependencies_check_box=install_tool_dependencies_check_box, containers_dict=containers_dict, @@ -1797,7 +1762,7 @@ changeset_revision = params.get( 'changeset_revision', None ) latest_changeset_revision = params.get( 'latest_changeset_revision', None ) latest_ctx_rev = params.get( 'latest_ctx_rev', None ) - repository = shed_util.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) + repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) if changeset_revision and latest_changeset_revision and latest_ctx_rev: if changeset_revision == latest_changeset_revision: message = "The installed repository named '%s' is current, there are no updates available. " % name diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -6,6 +6,7 @@ """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) + self.name = "reports" # Read config file and check for errors self.config = config.Configuration( **kwargs ) self.config.check() diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -103,14 +103,16 @@ </div></div> %if repository_dependencies_root_folder: - <div class="form-row"> - <label>Handle repository dependencies?</label> - ${install_repository_dependencies_check_box.get_html()} - <div class="toolParamHelp" style="clear: both;"> - Un-check to skip automatic installation of these additional repositories required by this repository. + %if install_repository_dependencies_check_box is not None: + <div class="form-row"> + <label>Handle repository dependencies?</label> + ${install_repository_dependencies_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Un-check to skip automatic installation of these additional repositories required by this repository. + </div></div> - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + %endif <div class="form-row"> %if repository_dependencies_root_folder: <p/> @@ -123,19 +125,21 @@ </div> %endif %if tool_dependencies_root_folder: - <div class="form-row"> - <label>Handle tool dependencies?</label> - <% disabled = trans.app.config.tool_dependency_dir is None %> - ${install_tool_dependencies_check_box.get_html( disabled=disabled )} - <div class="toolParamHelp" style="clear: both;"> - %if disabled: - Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies. - %else: - Un-check to skip automatic handling of these tool dependencies. - %endif + %if install_tool_dependencies_check_box is not None: + <div class="form-row"> + <label>Handle tool dependencies?</label> + <% disabled = trans.app.config.tool_dependency_dir is None %> + ${install_tool_dependencies_check_box.get_html( disabled=disabled )} + <div class="toolParamHelp" style="clear: both;"> + %if disabled: + Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies. + %else: + Un-check to skip automatic handling of these tool dependencies. + %endif + </div></div> - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + %endif <div class="form-row"> %if tool_dependencies_root_folder: <p/> diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -1,7 +1,19 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/webapps/community/repository/common.mako" import="*" /><%namespace file="/admin/tool_shed_repository/common.mako" import="*" /> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )} + ${container_javascripts()} +</%def> + <br/><br/><ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> @@ -91,218 +103,5 @@ </div><p/> %if not in_error_state: - <div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> - <div class="toolFormBody"> - <% - metadata = repository.metadata or {} - missing_tool_dependencies = repository.missing_tool_dependencies - installed_tool_dependencies = repository.installed_tool_dependencies - %> - %if missing_tool_dependencies: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Missing tool dependencies</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>version</b></td> - <td><b>type</b></td> - <td><b>status</b></td> - </tr> - %for tool_dependency in missing_tool_dependencies: - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( tool_dependency.id ) )}"> - ${tool_dependency.name} - </a> - </td> - <td>${tool_dependency.version}</td> - <td>${tool_dependency.type}</td> - <td>${tool_dependency.status}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if installed_tool_dependencies: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Installed tool dependencies<i> - click the name to browse the dependency installation directory</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>version</b></td> - <td><b>type</b></td> - </tr> - %for installed_tool_dependency in installed_tool_dependencies: - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( installed_tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}"> - ${installed_tool_dependency.name} - </a> - </td> - <td>${installed_tool_dependency.version}</td> - <td>${installed_tool_dependency.type}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'tools' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Tools</b><i> - click the name to view information about the tool</i></td> - </tr> - </table> - </div> - <div class="form-row"> - <% tool_dicts = metadata[ 'tools' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>description</b></td> - <td><b>version</b></td> - <td><b>requirements</b></td> - </tr> - %for tool_dict in tool_dicts: - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}"> - ${tool_dict[ 'name' ]} - </a> - </td> - <td>${tool_dict[ 'description' ]}</td> - <td>${tool_dict[ 'version' ]}</td> - <td> - <% - if 'requirements' in tool_dict: - requirements = tool_dict[ 'requirements' ] - else: - requirements = None - %> - %if requirements: - <% - requirements_str = '' - for requirement_dict in tool_dict[ 'requirements' ]: - requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) - requirements_str = requirements_str.rstrip( ', ' ) - %> - ${requirements_str} - %else: - none - %endif - </td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'workflows' in metadata: - ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is - ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Workflows</b><i> - click the name to import</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% workflow_tups = metadata[ 'workflows' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>steps</b></td> - <td><b>format-version</b></td> - <td><b>annotation</b></td> - </tr> - <% index = 0 %> - %for workflow_tup in workflow_tups: - <% - import os.path - relative_path = workflow_tup[ 0 ] - full_path = os.path.abspath( relative_path ) - workflow_dict = workflow_tup[ 1 ] - workflow_name = workflow_dict[ 'name' ] - ## Initially steps were not stored in the metadata record. - steps = workflow_dict.get( 'steps', [] ) - format_version = workflow_dict[ 'format-version' ] - annotation = workflow_dict[ 'annotation' ] - %> - <tr> - <td> - <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> - ${workflow_name} - <div popupmenu="workflow-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> - </div> - </div> - </td> - <td> - %if steps: - ${len( steps )} - %else: - unknown - %endif - </td> - <td>${format_version}</td> - <td>${annotation}</td> - </tr> - <% index += 1 %> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'datatypes' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Data types</b></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% datatypes_dicts = metadata[ 'datatypes' ] %> - <table class="grid"> - <tr> - <td><b>extension</b></td> - <td><b>type</b></td> - <td><b>mimetype</b></td> - <td><b>subclass</b></td> - </tr> - %for datatypes_dict in datatypes_dicts: - <tr> - <td>${datatypes_dict.get( 'extension', ' ' )}</td> - <td>${datatypes_dict.get( 'dtype', ' ' )}</td> - <td>${datatypes_dict.get( 'mimetype', ' ' )}</td> - <td>${datatypes_dict.get( 'subclass', ' ' )}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - </div> - </div> - <p/> + ${render_repository_items( repository.metadata, containers_dict, can_set_metadata=False )} %endif diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -2,6 +2,18 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> +<%namespace file="/webapps/community/repository/common.mako" import="*" /> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )} + ${container_javascripts()} +</%def> %if message: ${render_msg( message, status )} diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -208,14 +208,17 @@ folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) else: folder_label = "%s<i> - this repository requires installation of these additional repositories</i>" % folder_label + elif folder.label == 'Valid tools': + col_span_str = 'colspan="3"' + if folder.description: + folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) + else: + folder_label = "%s<i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i>" % folder_label elif folder.invalid_tools: folder_label = "%s<i> - click the tool config file name to see why the tool is invalid</i>" % folder_label elif folder.tool_dependencies: folder_label = "%s<i> - this repository's tools require handling of these dependencies</i>" % folder_label col_span_str = 'colspan="3"' - elif folder.valid_tools: - folder_label = "%s<i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i>" % folder_label - col_span_str = 'colspan="3"' elif folder.workflows: col_span_str = 'colspan="4"' %> @@ -302,7 +305,7 @@ %endif id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - %if invalid_tool.repository_id and invalid_tool.tool_config and invalid_tool.changeset_revision: + %if trans.webapp.name == 'community' and invalid_tool.repository_id and invalid_tool.tool_config and invalid_tool.changeset_revision: <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision )}"> ${invalid_tool.tool_config | h} </a> @@ -376,12 +379,20 @@ <th style="padding-left: ${pad+20}px;">${tool.name | h}</th> %else: <td style="padding-left: ${pad+20}px;"> - <div style="float:left;" class="menubutton split popup" id="tool-${encoded_id}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( tool.repository_id ), tool_config=tool.tool_config, changeset_revision=tool.changeset_revision )}">${tool.name | h}</a> - </div> - <div popupmenu="tool-${encoded_id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a> - </div> + %if tool.repository_id: + %if trans.webapp.name == 'community': + <div style="float:left;" class="menubutton split popup" id="tool-${encoded_id}-popup"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( tool.repository_id ), tool_config=tool.tool_config, changeset_revision=tool.changeset_revision )}">${tool.name | h}</a> + </div> + <div popupmenu="tool-${encoded_id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a> + </div> + %else: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a> + %endif + %else: + ${tool.name | h} + %endif </td> %endif <${cell_type}>${tool.description | h}</${cell_type}> @@ -459,7 +470,7 @@ %></%def> -<%def name="render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=False )"> +<%def name="render_repository_items( metadata, containers_dict, can_set_metadata=False )"><% from galaxy.tool_shed.encoding_util import tool_shed_encode @@ -472,6 +483,7 @@ readme_files_root_folder = containers_dict.get( 'readme_files', None ) repository_dependencies_root_folder = containers_dict.get( 'repository_dependencies', None ) tool_dependencies_root_folder = containers_dict.get( 'tool_dependencies', None ) + missing_tool_dependencies_root_folder = containers_dict.get( 'missing_tool_dependencies', None ) valid_tools_root_folder = containers_dict.get( 'valid_tools', none ) workflows_root_folder = containers_dict.get( 'workflows', None ) @@ -515,6 +527,13 @@ ${render_folder( tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} </table> %endif + %if missing_tool_dependencies_root_folder: + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="missing_tool_dependencies"> + ${render_folder( missing_tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + %endif </div></div> %endif diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -210,7 +210,7 @@ </form></div></div> -${render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=True )} +${render_repository_items( metadata, containers_dict, can_set_metadata=True )} <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div> diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -81,4 +81,4 @@ </div></div><p/> -${render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=False )} +${render_repository_items( metadata, containers_dict, can_set_metadata=False )} diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -188,7 +188,7 @@ %endif </div></div> -${render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=False )} +${render_repository_items( metadata, containers_dict, can_set_metadata=False )} %if repository.categories: <p/><div class="toolForm"> diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -67,10 +67,13 @@ for dependency in installed_repository.metadata[ 'tool_dependencies' ]: tool_dependency = installed_repository.metadata[ 'tool_dependencies' ][ dependency ] strings_displayed.extend( [ tool_dependency[ 'name' ], tool_dependency[ 'version' ], tool_dependency[ 'type' ] ] ) + """ + TODO: Uncomment these when Greg enhances the tool dependencies and missing tool dependencies containers to display the status. if dependencies_installed: strings_displayed.append( 'Installed' ) else: strings_displayed.append( 'Never installed' ) + """ url = '/admin_toolshed/manage_repository?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 test/tool_shed/functional/test_1000_install_basic_repository.py --- a/test/tool_shed/functional/test_1000_install_basic_repository.py +++ b/test/tool_shed/functional/test_1000_install_basic_repository.py @@ -55,7 +55,7 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.verify_installed_repository_on_browse_page( installed_repository ) self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Tools', 'Filter1' ] ) + strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0030_verify_installed_repository_metadata( self ): '''Verify that resetting the metadata on an installed repository does not change the metadata.''' diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -74,7 +74,7 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) self.verify_installed_repository_on_browse_page( installed_repository ) self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Tools', 'FreeBayes' ] ) + strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0020_verify_installed_repository_metadata( self ): diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -69,7 +69,7 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0020', common.test_user_1_name ) self.verify_installed_repository_on_browse_page( installed_repository ) self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Tools', 'antigenic' ] ) + strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0020_verify_installed_repository_metadata( self ): diff -r 075ff805a33a830244c4647fc9cefec663eff2b4 -r 759d96f950b8825bcce157cdf5efbabaa0221b11 test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py @@ -111,7 +111,7 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name ) self.verify_installed_repository_on_browse_page( installed_repository ) self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Tools', 'antigenic' ] ) + strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 19 Dec '12

19 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9785184717ac/ changeset: 9785184717ac user: carlfeberhard date: 2012-12-19 21:46:55 summary: history panel: fix delete function to use show_deleted affected #: 4 files diff -r 1fe77194bce0c78294f2c1f10fc231faf2006a2c -r 9785184717ac1fcc589c0183f2873d40ed993c57 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -44,7 +44,8 @@ this.expanded = attributes.expanded || false; // re-render the entire view on any model change - this.model.bind( 'change', this.render, this ); + this.model.bind( 'change', this.render , this ); + //this.bind( 'all', function( event ){ // this.log( event ); //}, this ); diff -r 1fe77194bce0c78294f2c1f10fc231faf2006a2c -r 9785184717ac1fcc589c0183f2873d40ed993c57 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -118,9 +118,6 @@ id : 'historyItemDeleter-' + this.model.get( 'id' ), icon_class : 'delete', on_click : function() { - // Provide feedback by hiding from view immediately. - self.$el.slideUp(); - // Delete the dataset on the server and update HDA + view depending on success/failure. // FIXME: when HDA-delete is implemented in the API, can call set(), then save directly // on the model. @@ -134,13 +131,13 @@ }, success: function() { // FIXME: setting model attribute causes re-rendering, which is unnecessary. - self.model.set( 'deleted', true ); - self.$el.remove(); + //self.$el.remove(); + self.model.set({ deleted: true }); } }); // Return false so that anchor action (page reload) does not happen. - return false; + //return false; } }; if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ diff -r 1fe77194bce0c78294f2c1f10fc231faf2006a2c -r 9785184717ac1fcc589c0183f2873d40ed993c57 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -163,6 +163,11 @@ this.model.hdas.bind( 'add', this.add, this ); this.model.hdas.bind( 'reset', this.addAll, this ); + // when a hda model is (un)deleted or (un)hidden, re-render entirely + //TODO??: purged + //TODO??: could be more selective here + this.model.hdas.bind( 'change:deleted change:hidden', this.render, this ); + // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, // then: remove it from the collection if the panel is set to NOT show hidden datasets this.model.hdas.bind( 'change:state', @@ -292,6 +297,7 @@ // fade out existing, swap with the new, fade in, set up behaviours $( historyView ).queue( setUpQueueName, function( next ){ historyView.$el.fadeOut( 'fast', function(){ next(); }); + //historyView.$el.show( function(){ next(); }); }); $( historyView ).queue( setUpQueueName, function( next ){ // swap over from temp div newRender @@ -299,6 +305,7 @@ historyView.$el.append( newRender.children() ); historyView.$el.fadeIn( 'fast', function(){ next(); }); + //historyView.$el.show( function(){ next(); }); }); $( historyView ).queue( setUpQueueName, function( next ){ this.log( historyView + ' rendered:', historyView.$el ); diff -r 1fe77194bce0c78294f2c1f10fc231faf2006a2c -r 9785184717ac1fcc589c0183f2873d40ed993c57 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -144,8 +144,7 @@ #TODO: via api #TODO: show deleted handled by history - 'delete' : h.url_for( controller='dataset', action='delete', - dataset_id=encoded_id_template, show_deleted_on_refresh=show_deleted ), + 'delete' : h.url_for( controller='dataset', action='delete_async', dataset_id=encoded_id_template ), # ................................................................ download links (and associated meta files), 'download' : h.url_for( controller='/dataset', action='display', https://bitbucket.org/galaxy/galaxy-central/changeset/075ff805a33a/ changeset: 075ff805a33a user: carlfeberhard date: 2012-12-19 21:49:03 summary: pack scripts affected #: 2 files diff -r 9785184717ac1fcc589c0183f2873d40ed993c57 -r 075ff805a33a830244c4647fc9cefec663eff2b4 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 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){a.$el.slideUp();$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set("deleted",true);a.$el.remove()}});return false}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 9785184717ac1fcc589c0183f2873d40ed993c57 -r 075ff805a33a830244c4647fc9cefec663eff2b4 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHda(c)}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},removeHda:function(a,c){var b=this.hdaViews[a.get("id")];b.$el.fadeOut("fast",function(){b.$el.remove();if(c){c()}});this.model.hdas.remove(a)},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted change:hidden",this.render,this);this.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHda(c)}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},removeHda:function(a,c){var b=this.hdaViews[a.get("id")];b.$el.fadeOut("fast",function(){b.$el.remove();if(c){c()}});this.model.hdas.remove(a)},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: .hgignore: ignore test/selenium related jar and html
by Bitbucket 19 Dec '12

19 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1fe77194bce0/ changeset: 1fe77194bce0 user: carlfeberhard date: 2012-12-19 18:01:57 summary: .hgignore: ignore test/selenium related jar and html affected #: 1 file diff -r ba540beb1cedb0a5040789036bd67359fc0fa64b -r 1fe77194bce0c78294f2c1f10fc231faf2006a2c .hgignore --- a/.hgignore +++ b/.hgignore @@ -74,6 +74,10 @@ */variables.less static/june_2007_style/blue/base_sprites.less +# Testing +selenium-server.jar +selenium_results.html + # Documentation build files. doc/build 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 Bitbucket 19 Dec '12

19 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36ad8aa7b922/ changeset: 36ad8aa7b922 user: inithello date: 2012-12-19 17:08:26 summary: Fix for reinstalling tool shed repository with readme files. affected #: 1 file diff -r cda19f585a15241a1ee91a795a995a8f1dcca188 -r 36ad8aa7b922a0ea32d27c1b2506c9d715ad53bb lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1569,11 +1569,13 @@ raw_text = response.read() response.close() readme_files_dict = from_json_string( raw_text ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + repository_dependencies = metadata.get( 'repository_dependencies', None ) containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, - repository_name=name, - repository_owner=repository_owner, - changeset_revision=changeset_revision, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + changeset_revision=tool_shed_repository.installed_changeset_revision, readme_files_dict=readme_files_dict, repository_dependencies=repository_dependencies, tool_dependencies=tool_dependencies ) https://bitbucket.org/galaxy/galaxy-central/changeset/ba540beb1ced/ changeset: ba540beb1ced user: inithello date: 2012-12-19 17:14:44 summary: Merged changes from galaxy-dist-central. affected #: 1 file diff -r 715a7fe08b4c415e422c179250984d727d11673f -r ba540beb1cedb0a5040789036bd67359fc0fa64b lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1569,11 +1569,13 @@ raw_text = response.read() response.close() readme_files_dict = from_json_string( raw_text ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + repository_dependencies = metadata.get( 'repository_dependencies', None ) containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, - repository_name=name, - repository_owner=repository_owner, - changeset_revision=changeset_revision, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + changeset_revision=tool_shed_repository.installed_changeset_revision, readme_files_dict=readme_files_dict, repository_dependencies=repository_dependencies, tool_dependencies=tool_dependencies ) 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: jgoecks: Qualifier fix.
by Bitbucket 19 Dec '12

19 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/715a7fe08b4c/ changeset: 715a7fe08b4c user: jgoecks date: 2012-12-19 14:43:57 summary: Qualifier fix. affected #: 1 file diff -r eae248415389203907b5b951f139a200024ae069 -r 715a7fe08b4c415e422c179250984d727d11673f lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -50,7 +50,7 @@ elif isinstance( original_dataset.datatype, Vcf ): data_provider_class = genome.RawVcfDataProvider elif isinstance( original_dataset.datatype, Tabular ): - data_provider_class = genome.ColumnDataProvider + data_provider_class = ColumnDataProvider elif isinstance( original_dataset.datatype, ( Nexus, Newick, Phyloxml ) ): data_provider_class = genome.PhylovizDataProvider 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: clements: First iteration of updating Sphinx RST files. These describe classes and modules (and ...) and are used to generate the Sphinx code documentation. However, they are not updated automatically.
by Bitbucket 18 Dec '12

18 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/eae248415389/ changeset: eae248415389 user: clements date: 2012-12-18 22:27:20 summary: First iteration of updating Sphinx RST files. These describe classes and modules (and ...) and are used to generate the Sphinx code documentation. However, they are not updated automatically. Add the patch.py to automate some of the RST update process, but it is still pretty brutal. Look for cleanup in the next few releases. affected #: 9 files diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/Makefile --- a/doc/Makefile +++ b/doc/Makefile @@ -6,6 +6,9 @@ SPHINXBUILD = sphinx-build PAPER = BUILDDIR = build +UPDATEWORKDIR = /tmp/galaxySphinxUpdate +UPDATEWORKSOURCELIB = $(UPDATEWORKDIR)/source/lib +SPHINXAPIDOC = sphinx-apidoc # Internal variables. PAPEROPT_a4 = -D latex_paper_size=a4 @@ -21,7 +24,7 @@ $(TOOLDATASHAREDDIR)/ncbi/builds.txt \ $(TOOLDATASHAREDDIR)/ucsc/publicbuilds.txt -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext updaterst # Sphinx wants the build files to be there; Copy the sample files into @@ -51,9 +54,13 @@ @echo " changes to make an overview of all changed/added/deprecated items" @echo " linkcheck to check all external links for integrity" @echo " doctest to run all doctests embedded in the documentation (if enabled)" + @echo " updaterst to update sphinx rst to reflect code structure changes" + +# might also want to do +# cd source/lib; hg revert; rm *.rst.orig; or not. clean: - -rm -rf $(BUILDDIR)/* + -rm -rf $(BUILDDIR)/* $(UPDATEWORKDIR) html: $(TOOLDATABUILDFILES) $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @@ -165,3 +172,20 @@ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest @echo "Testing of doctests in the sources finished, look at the " \ "results in $(BUILDDIR)/doctest/output.txt." + +# Targets for updating the structure of the Sphinx RST doc for lib/ + +$(UPDATEWORKSOURCELIB): + mkdir -p $(UPDATEWORKSOURCELIB) + +# Create a fresh version of the RST files for the lib, and then create a +# unified patch file (ignore all emacs leftovers). +# Feed that to our custom version of patch.py, which applies patches that +# are only adds, and reports everything else to the user to deal with manually +# +# Note: this is still a very rough process. the run of patch.py gets some +# errors that don't mean anything to us. And the manual process is not fun. +updaterst: $(UPDATEWORKSOURCELIB) + $(SPHINXAPIDOC) -o $(UPDATEWORKSOURCELIB) ../lib + -diff -x '*.rst~' -ru source/lib $(UPDATEWORKSOURCELIB) > $(UPDATEWORKDIR)/alldifs.patch + ./patch.py $(UPDATEWORKDIR)/alldifs.patch diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/patch.py --- /dev/null +++ b/doc/patch.py @@ -0,0 +1,1085 @@ +#!/usr/bin/env python +""" Patch utility to apply unified diffs + + Brute-force line-by-line non-recursive parsing + + Copyright (c) 2008-2012 anatoly techtonik + Available under the terms of MIT license + + Project home: http://code.google.com/p/python-patch/ + + + $Id: patch.py 181 2012-11-23 16:03:05Z techtonik $ + $HeadURL: https://python-patch.googlecode.com/svn/trunk/patch.py $ + + This program needs further tweaking for how we use it at Galaxy. +""" + +__author__ = "anatoly techtonik <techtonik(a)gmail.com>" +__version__ = "1.12.11" + +import copy +import logging +import re +# cStringIO doesn't support unicode in 2.5 +from StringIO import StringIO +import urllib2 + +from os.path import exists, isfile, abspath +import os +import shutil + +#------------------------------------------------ +# Logging is controlled by logger named after the +# module name (e.g. 'patch' for patch.py module) + +debugmode = False + +logger = logging.getLogger(__name__) + +debug = logger.debug +info = logger.info +warning = logger.warning + +class NullHandler(logging.Handler): + """ Copied from Python 2.7 to avoid getting + `No handlers could be found for logger "patch"` + http://bugs.python.org/issue16539 + """ + def handle(self, record): + pass + def emit(self, record): + pass + def createLock(self): + self.lock = None + +logger.addHandler(NullHandler()) + +#------------------------------------------------ +# Constants for Patch/PatchSet types + +DIFF = PLAIN = "plain" +GIT = "git" +HG = MERCURIAL = "mercurial" +SVN = SUBVERSION = "svn" +# mixed type is only actual when PatchSet contains +# Patches of different type +MIXED = MIXED = "mixed" + + +#------------------------------------------------ +# Helpers (these could come with Python stdlib) + +# x...() function are used to work with paths in +# cross-platform manner - all paths use forward +# slashes even on Windows. + +def xisabs(filename): + """ Cross-platform version of `os.path.isabs()` + Returns True if `filename` is absolute on + Linux, OS X or Windows. + """ + if filename.startswith('/'): # Linux/Unix + return True + elif filename.startswith('\\'): # Windows + return True + elif re.match(r'\w:[\\/]', filename): # Windows + return True + return False + +def xnormpath(path): + """ Cross-platform version of os.path.normpath """ + return os.path.normpath(path).replace(os.sep, '/') + +def xstrip(filename): + """ Make relative path out of absolute by stripping + prefixes used on Linux, OS X and Windows. + + This function is critical for security. + """ + while xisabs(filename): + # strip windows drive with all slashes + if re.match(r'\w:[\\/]', filename): + filename = re.sub(r'^\w+:[\\/]+', '', filename) + # strip all slashes + elif re.match(r'[\\/]', filename): + filename = re.sub(r'^[\\/]+', '', filename) + return filename + +#----------------------------------------------- +# Main API functions + +def fromfile(filename): + """ Parse patch file. If successful, returns + PatchSet() object. Otherwise returns False. + """ + patchset = PatchSet() + debug("reading %s" % filename) + fp = open(filename, "rb") + res = patchset.parse(fp) + fp.close() + if res == True: + return patchset + return False + + +def fromstring(s): + """ Parse text string and return PatchSet() + object (or False if parsing fails) + """ + ps = PatchSet( StringIO(s) ) + if ps.errors == 0: + return ps + return False + + +def fromurl(url): + """ Parse patch from an URL, return False + if an error occured. Note that this also + can throw urlopen() exceptions. + """ + ps = PatchSet( urllib2.urlopen(url) ) + if ps.errors == 0: + return ps + return False + + +# --- Utility functions --- +# [ ] reuse more universal pathsplit() +def pathstrip(path, n): + """ Strip n leading components from the given path """ + pathlist = [path] + while os.path.dirname(pathlist[0]) != '': + pathlist[0:1] = os.path.split(pathlist[0]) + return '/'.join(pathlist[n:]) +# --- /Utility function --- + + +class Hunk(object): + """ Parsed hunk data container (hunk starts with @@ -R +R @@) """ + + def __init__(self): + self.startsrc=None #: line count starts with 1 + self.linessrc=None + self.starttgt=None + self.linestgt=None + self.invalid=False + self.hasplus=False # True if any "+" lines in hunk + self.hasminus=False # True if any "-" lines in hunk + self.text=[] + + def originalText(self): + + return("@@ -" + str(self.startsrc) + + "," + str(self.linessrc) + + " +" + str(self.starttgt) + + "," + str(self.linestgt) + + "\n" + + self.printableText()) + + def printableText(self): + """Reformat text into printable text""" + + # yeah, there must be a better way to do this. + printable = "" + for line in self.text: + printable += line + + return printable + + + +# def apply(self, estream): +# """ write hunk data into enumerable stream +# return strings one by one until hunk is +# over +# +# enumerable stream are tuples (lineno, line) +# where lineno starts with 0 +# """ +# pass + + +class Patch(object): + """ Patch for a single file """ + def __init__(self): + self.source = None + self.target = None + self.hunks = [] + self.hunkends = [] + self.header = [] + + self.type = None + + +class PatchSet(object): + + def __init__(self, stream=None): + # --- API accessible fields --- + + # name of the PatchSet (filename or ...) + self.name = None + # patch set type - one of constants + self.type = None + + # list of Patch objects + self.items = [] + + self.errors = 0 # fatal parsing errors + self.warnings = 0 # non-critical warnings + # --- /API --- + + if stream: + self.parse(stream) + + def __len__(self): + return len(self.items) + + def parse(self, stream): + """ parse unified diff + return True on success + """ + lineends = dict(lf=0, crlf=0, cr=0) + nexthunkno = 0 #: even if index starts with 0 user messages number hunks from 1 + + p = None + hunk = None + # hunkactual variable is used to calculate hunk lines for comparison + hunkactual = dict(linessrc=None, linestgt=None) + + + class wrapumerate(enumerate): + """Enumerate wrapper that uses boolean end of stream status instead of + StopIteration exception, and properties to access line information. + """ + + def __init__(self, *args, **kwargs): + # we don't call parent, it is magically created by __new__ method + + self._exhausted = False + self._lineno = False # after end of stream equal to the num of lines + self._line = False # will be reset to False after end of stream + + def next(self): + """Try to read the next line and return True if it is available, + False if end of stream is reached.""" + if self._exhausted: + return False + + try: + self._lineno, self._line = super(wrapumerate, self).next() + except StopIteration: + self._exhausted = True + self._line = False + return False + return True + + @property + def is_empty(self): + return self._exhausted + + @property + def line(self): + return self._line + + @property + def lineno(self): + return self._lineno + + # define states (possible file regions) that direct parse flow + headscan = True # start with scanning header + filenames = False # lines starting with --- and +++ + + hunkhead = False # @@ -R +R @@ sequence + hunkbody = False # + hunkskip = False # skipping invalid hunk mode + + hunkparsed = False # state after successfully parsed hunk + + # regexp to match start of hunk, used groups - 1,3,4,6 + re_hunk_start = re.compile("^@@ -(\d+)(,(\d+))? \+(\d+)(,(\d+))?") + + self.errors = 0 + # temp buffers for header and filenames info + header = [] + srcname = None + tgtname = None + + # start of main cycle + # each parsing block already has line available in fe.line + fe = wrapumerate(stream) + while fe.next(): + + # -- deciders: these only switch state to decide who should process + # -- line fetched at the start of this cycle + if hunkparsed: + hunkparsed = False + if re_hunk_start.match(fe.line): + hunkhead = True + elif fe.line.startswith("--- "): + filenames = True + else: + headscan = True + # -- ------------------------------------ + + # read out header + if headscan: + while not fe.is_empty and not fe.line.startswith("--- "): + header.append(fe.line) + fe.next() + if fe.is_empty: + if p == None: + debug("no patch data found") # error is shown later + self.errors += 1 + else: + info("%d unparsed bytes left at the end of stream" % len(''.join(header))) + self.warnings += 1 + # TODO check for \No new line at the end.. + # TODO test for unparsed bytes + # otherwise error += 1 + # this is actually a loop exit + continue + + headscan = False + # switch to filenames state + filenames = True + + line = fe.line + lineno = fe.lineno + + + # hunkskip and hunkbody code skipped until definition of hunkhead is parsed + if hunkbody: + # [x] treat empty lines inside hunks as containing single space + # (this happens when diff is saved by copy/pasting to editor + # that strips trailing whitespace) + if line.strip("\r\n") == "": + debug("expanding empty line in a middle of hunk body") + self.warnings += 1 + line = ' ' + line + + # process line first + if re.match(r"^[- \+\\]", line): + # gather stats about line endings + if line.endswith("\r\n"): + p.hunkends["crlf"] += 1 + elif line.endswith("\n"): + p.hunkends["lf"] += 1 + elif line.endswith("\r"): + p.hunkends["cr"] += 1 + + if line.startswith("-"): + hunkactual["linessrc"] += 1 + hunk.hasminus = True + elif line.startswith("+"): + hunkactual["linestgt"] += 1 + hunk.hasplus = True + elif not line.startswith("\\"): + hunkactual["linessrc"] += 1 + hunkactual["linestgt"] += 1 + hunk.text.append(line) + # todo: handle \ No newline cases + else: + warning("invalid hunk no.%d at %d for target file %s" % (nexthunkno, lineno+1, p.target)) + # add hunk status node + hunk.invalid = True + p.hunks.append(hunk) + self.errors += 1 + # switch to hunkskip state + hunkbody = False + hunkskip = True + + # check exit conditions + if hunkactual["linessrc"] > hunk.linessrc or hunkactual["linestgt"] > hunk.linestgt: + warning("extra lines for hunk no.%d at %d for target %s" % (nexthunkno, lineno+1, p.target)) + # add hunk status node + hunk.invalid = True + p.hunks.append(hunk) + self.errors += 1 + # switch to hunkskip state + hunkbody = False + hunkskip = True + elif hunk.linessrc == hunkactual["linessrc"] and hunk.linestgt == hunkactual["linestgt"]: + # hunk parsed successfully + p.hunks.append(hunk) + # switch to hunkparsed state + hunkbody = False + hunkparsed = True + + # detect mixed window/unix line ends + ends = p.hunkends + if ((ends["cr"]!=0) + (ends["crlf"]!=0) + (ends["lf"]!=0)) > 1: + warning("inconsistent line ends in patch hunks for %s" % p.source) + self.warnings += 1 + if debugmode: + debuglines = dict(ends) + debuglines.update(file=p.target, hunk=nexthunkno) + debug("crlf: %(crlf)d lf: %(lf)d cr: %(cr)d\t - file: %(file)s hunk: %(hunk)d" % debuglines) + # fetch next line + continue + + if hunkskip: + if re_hunk_start.match(line): + # switch to hunkhead state + hunkskip = False + hunkhead = True + elif line.startswith("--- "): + # switch to filenames state + hunkskip = False + filenames = True + if debugmode and len(self.items) > 0: + debug("- %2d hunks for %s" % (len(p.hunks), p.source)) + + if filenames: + if line.startswith("--- "): + if srcname != None: + # XXX testcase + warning("skipping false patch for %s" % srcname) + srcname = None + # XXX header += srcname + # double source filename line is encountered + # attempt to restart from this second line + re_filename = "^--- ([^\t]+)" + match = re.match(re_filename, line) + # todo: support spaces in filenames + if match: + srcname = match.group(1).strip() + else: + warning("skipping invalid filename at line %d" % lineno) + self.errors += 1 + # XXX p.header += line + # switch back to headscan state + filenames = False + headscan = True + elif not line.startswith("+++ "): + if srcname != None: + warning("skipping invalid patch with no target for %s" % srcname) + self.errors += 1 + srcname = None + # XXX header += srcname + # XXX header += line + else: + # this should be unreachable + warning("skipping invalid target patch") + filenames = False + headscan = True + else: + if tgtname != None: + # XXX seems to be a dead branch + warning("skipping invalid patch - double target at line %d" % lineno) + self.errors += 1 + srcname = None + tgtname = None + # XXX header += srcname + # XXX header += tgtname + # XXX header += line + # double target filename line is encountered + # switch back to headscan state + filenames = False + headscan = True + else: + re_filename = "^\+\+\+ ([^\t]+)" + match = re.match(re_filename, line) + if not match: + warning("skipping invalid patch - no target filename at line %d" % lineno) + self.errors += 1 + srcname = None + # switch back to headscan state + filenames = False + headscan = True + else: + if p: # for the first run p is None + self.items.append(p) + p = Patch() + p.source = srcname + srcname = None + p.target = match.group(1).strip() + p.header = header + header = [] + # switch to hunkhead state + filenames = False + hunkhead = True + nexthunkno = 0 + p.hunkends = lineends.copy() + continue + + if hunkhead: + match = re.match("^@@ -(\d+)(,(\d+))? \+(\d+)(,(\d+))?", line) + if not match: + if not p.hunks: + warning("skipping invalid patch with no hunks for file %s" % p.source) + self.errors += 1 + # XXX review switch + # switch to headscan state + hunkhead = False + headscan = True + continue + else: + # TODO review condition case + # switch to headscan state + hunkhead = False + headscan = True + else: + hunk = Hunk() + hunk.startsrc = int(match.group(1)) + hunk.linessrc = 1 + if match.group(3): hunk.linessrc = int(match.group(3)) + hunk.starttgt = int(match.group(4)) + hunk.linestgt = 1 + if match.group(6): hunk.linestgt = int(match.group(6)) + hunk.invalid = False + hunk.text = [] + + hunkactual["linessrc"] = hunkactual["linestgt"] = 0 + + # switch to hunkbody state + hunkhead = False + hunkbody = True + nexthunkno += 1 + continue + + # /while fe.next() + + if p: + self.items.append(p) + + if not hunkparsed: + if hunkskip: + warning("warning: finished with errors, some hunks may be invalid") + elif headscan: + if len(self.items) == 0: + warning("error: no patch data found!") + return False + else: # extra data at the end of file + pass + else: + warning("error: patch stream is incomplete!") + self.errors += 1 + if len(self.items) == 0: + return False + + if debugmode and len(self.items) > 0: + debug("- %2d hunks for %s" % (len(p.hunks), p.source)) + + # XXX fix total hunks calculation + debug("total files: %d total hunks: %d" % (len(self.items), + sum(len(p.hunks) for p in self.items))) + + # ---- detect patch and patchset types ---- + for idx, p in enumerate(self.items): + self.items[idx].type = self._detect_type(p) + + types = set([p.type for p in self.items]) + if len(types) > 1: + self.type = MIXED + else: + self.type = types.pop() + # -------- + + self._normalize_filenames() + + return (self.errors == 0) + + def _detect_type(self, p): + """ detect and return type for the specified Patch object + analyzes header and filenames info + + NOTE: must be run before filenames are normalized + """ + + # check for SVN + # - header starts with Index: + # - next line is ===... delimiter + # - filename is followed by revision number + # TODO add SVN revision + if (len(p.header) > 1 and p.header[-2].startswith("Index: ") + and p.header[-1].startswith("="*67)): + return SVN + + # common checks for both HG and GIT + DVCS = ((p.source.startswith('a/') or p.source == '/dev/null') + and (p.target.startswith('b/') or p.target == '/dev/null')) + + # GIT type check + # - header[-2] is like "diff --git a/oldname b/newname" + # - header[-1] is like "index <hash>..<hash><mode>" + # TODO add git rename diffs and add/remove diffs + # add git diff with spaced filename + # TODO http://www.kernel.org/pub/software/scm/git/docs/git-diff.html + + # detect the start of diff header - there might be some comments before + if len(p.header) > 1: + for idx in reversed(range(len(p.header))): + if p.header[idx].startswith("diff --git"): + break + if re.match(r'diff --git a/[\w/.]+ b/[\w/.]+', p.header[idx]): + if (idx+1 < len(p.header) + and re.match(r'index \w{7}..\w{7} \d{6}', p.header[idx+1])): + if DVCS: + return GIT + + # HG check + # + # - for plain HG format header is like "diff -r b2d9961ff1f5 filename" + # - for Git-style HG patches it is "diff --git a/oldname b/newname" + # - filename starts with a/, b/ or is equal to /dev/null + # - exported changesets also contain the header + # # HG changeset patch + # # User name(a)example.com + # ... + # TODO add MQ + # TODO add revision info + if len(p.header) > 0: + if DVCS and re.match(r'diff -r \w{12} .*', p.header[-1]): + return HG + if DVCS and p.header[-1].startswith('diff --git a/'): + if len(p.header) == 1: # native Git patch header len is 2 + return HG + elif p.header[0].startswith('# HG changeset patch'): + return HG + + return PLAIN + + + def _normalize_filenames(self): + """ sanitize filenames, normalizing paths, i.e.: + 1. strip a/ and b/ prefixes from GIT and HG style patches + 2. remove all references to parent directories (with warning) + 3. translate any absolute paths to relative (with warning) + + [x] always use forward slashes to be crossplatform + (diff/patch were born as a unix utility after all) + + return None + """ + for i,p in enumerate(self.items): + if p.type in (HG, GIT): + # TODO: figure out how to deal with /dev/null entries + debug("stripping a/ and b/ prefixes") + if p.source != '/dev/null': + if not p.source.startswith("a/"): + warning("invalid source filename") + else: + p.source = p.source[2:] + if p.target != '/dev/null': + if not p.target.startswith("b/"): + warning("invalid target filename") + else: + p.target = p.target[2:] + + p.source = xnormpath(p.source) + p.target = xnormpath(p.target) + + sep = '/' # sep value can be hardcoded, but it looks nice this way + + # references to parent are not allowed + if p.source.startswith(".." + sep): + warning("error: stripping parent path for source file patch no.%d" % (i+1)) + self.warnings += 1 + while p.source.startswith(".." + sep): + p.source = p.source.partition(sep)[2] + if p.target.startswith(".." + sep): + warning("error: stripping parent path for target file patch no.%d" % (i+1)) + self.warnings += 1 + while p.target.startswith(".." + sep): + p.target = p.target.partition(sep)[2] + # absolute paths are not allowed + if xisabs(p.source) or xisabs(p.target): + warning("error: absolute paths are not allowed - file no.%d" % (i+1)) + self.warnings += 1 + if xisabs(p.source): + warning("stripping absolute path from source name '%s'" % p.source) + p.source = xstrip(p.source) + if xisabs(p.target): + warning("stripping absolute path from target name '%s'" % p.target) + p.target = xstrip(p.target) + + self.items[i].source = p.source + self.items[i].target = p.target + + + def diffstat(self): + """ calculate diffstat and return as a string + Notes: + - original diffstat ouputs target filename + - single + or - shouldn't escape histogram + """ + names = [] + insert = [] + delete = [] + namelen = 0 + maxdiff = 0 # max number of changes for single file + # (for histogram width calculation) + for patch in self.items: + i,d = 0,0 + for hunk in patch.hunks: + for line in hunk.text: + if line.startswith('+'): + i += 1 + elif line.startswith('-'): + d += 1 + names.append(patch.target) + insert.append(i) + delete.append(d) + namelen = max(namelen, len(patch.target)) + maxdiff = max(maxdiff, i+d) + output = '' + statlen = len(str(maxdiff)) # stats column width + for i,n in enumerate(names): + # %-19s | %-4d %s + format = " %-" + str(namelen) + "s | %" + str(statlen) + "s %s\n" + + hist = '' + # -- calculating histogram -- + width = len(format % ('', '', '')) + histwidth = max(2, 80 - width) + if maxdiff < histwidth: + hist = "+"*insert[i] + "-"*delete[i] + else: + iratio = (float(insert[i]) / maxdiff) * histwidth + dratio = (float(delete[i]) / maxdiff) * histwidth + + # make sure every entry gets at least one + or - + iwidth = 1 if 0 < iratio < 1 else int(iratio) + dwidth = 1 if 0 < dratio < 1 else int(dratio) + #print iratio, dratio, iwidth, dwidth, histwidth + hist = "+"*int(iwidth) + "-"*int(dwidth) + # -- /calculating +- histogram -- + output += (format % (names[i], insert[i] + delete[i], hist)) + + output += (" %d files changed, %d insertions(+), %d deletions(-)" + % (len(names), sum(insert), sum(delete))) + return output + + + def apply(self, strip=0): + """ apply parsed patch + return True on success + """ + + total = len(self.items) + errors = 0 + if strip: + # [ ] test strip level exceeds nesting level + # [ ] test the same only for selected files + # [ ] test if files end up being on the same level + try: + strip = int(strip) + except ValueError: + errors += 1 + warning("error: strip parameter '%s' must be an integer" % strip) + strip = 0 + + #for fileno, filename in enumerate(self.source): + for i,p in enumerate(self.items): + f2patch = p.source + if strip: + debug("stripping %s leading component from '%s'" % (strip, f2patch)) + f2patch = pathstrip(f2patch, strip) + if not exists(f2patch): + f2patch = p.target + if strip: + debug("stripping %s leading component from '%s'" % (strip, f2patch)) + f2patch = pathstrip(f2patch, strip) + if not exists(f2patch): + warning("source/target file does not exist\n--- %s\n+++ %s" % (p.source, f2patch)) + errors += 1 + continue + if not isfile(f2patch): + warning("not a file - %s" % f2patch) + errors += 1 + continue + filename = f2patch + + debug("processing %d/%d:\t %s" % (i+1, total, filename)) + + # validate before patching + f2fp = open(filename) + hunkno = 0 + hunk = p.hunks[hunkno] + hunkfind = [] + hunkreplace = [] + validhunks = 0 + canpatch = False + for lineno, line in enumerate(f2fp): + if lineno+1 < hunk.startsrc: + continue + elif lineno+1 == hunk.startsrc: + hunkfind = [x[1:].rstrip("\r\n") for x in hunk.text if x[0] in " -"] + hunkreplace = [x[1:].rstrip("\r\n") for x in hunk.text if x[0] in " +"] + #pprint(hunkreplace) + hunklineno = 0 + + # todo \ No newline at end of file + + # check hunks in source file + if lineno+1 < hunk.startsrc+len(hunkfind)-1: + if line.rstrip("\r\n") == hunkfind[hunklineno]: + hunklineno+=1 + else: + info("file %d/%d:\t %s" % (i+1, total, filename)) + info(" hunk no.%d doesn't match source file at line %d" % (hunkno+1, lineno)) + info(" expected: %s" % hunkfind[hunklineno]) + info(" actual : %s" % line.rstrip("\r\n")) + # not counting this as error, because file may already be patched. + # check if file is already patched is done after the number of + # invalid hunks if found + # TODO: check hunks against source/target file in one pass + # API - check(stream, srchunks, tgthunks) + # return tuple (srcerrs, tgterrs) + + # continue to check other hunks for completeness + hunkno += 1 + if hunkno < len(p.hunks): + hunk = p.hunks[hunkno] + continue + else: + break + + # check if processed line is the last line + if lineno+1 == hunk.startsrc+len(hunkfind)-1: + debug(" hunk no.%d for file %s -- is ready to be patched" % (hunkno+1, filename)) + hunkno+=1 + validhunks+=1 + if hunkno < len(p.hunks): + hunk = p.hunks[hunkno] + else: + if validhunks == len(p.hunks): + # patch file + canpatch = True + break + else: + if hunkno < len(p.hunks): + warning("premature end of source file %s at hunk %d" % (filename, hunkno+1)) + errors += 1 + + f2fp.close() + + if validhunks < len(p.hunks): + if self._match_file_hunks(filename, p.hunks): + warning("already patched %s" % filename) + else: + warning("source file is different - %s" % filename) + errors += 1 + if canpatch: + backupname = filename+".orig" + if exists(backupname): + warning("can't backup original file to %s - aborting" % backupname) + else: + import shutil + shutil.move(filename, backupname) + if self.write_hunks(backupname, filename, p.hunks): + info("successfully patched %d/%d:\t %s" % (i+1, total, filename)) + os.unlink(backupname) + else: + errors += 1 + warning("error patching file %s" % filename) + shutil.copy(filename, filename+".invalid") + warning("invalid version is saved to %s" % filename+".invalid") + # todo: proper rejects + shutil.move(backupname, filename) + + # todo: check for premature eof + return (errors == 0) + + + def can_patch(self, filename): + """ Check if specified filename can be patched. Returns None if file can + not be found among source filenames. False if patch can not be applied + clearly. True otherwise. + + :returns: True, False or None + """ + filename = abspath(filename) + for p in self.items: + if filename == abspath(p.source): + return self._match_file_hunks(filename, p.hunks) + return None + + + def _match_file_hunks(self, filepath, hunks): + matched = True + fp = open(abspath(filepath)) + + class NoMatch(Exception): + pass + + lineno = 1 + line = fp.readline() + hno = None + try: + for hno, h in enumerate(hunks): + # skip to first line of the hunk + while lineno < h.starttgt: + if not len(line): # eof + debug("check failed - premature eof before hunk: %d" % (hno+1)) + raise NoMatch + line = fp.readline() + lineno += 1 + for hline in h.text: + if hline.startswith("-"): + continue + if not len(line): + debug("check failed - premature eof on hunk: %d" % (hno+1)) + # todo: \ No newline at the end of file + raise NoMatch + if line.rstrip("\r\n") != hline[1:].rstrip("\r\n"): + debug("file is not patched - failed hunk: %d" % (hno+1)) + raise NoMatch + line = fp.readline() + lineno += 1 + + except NoMatch: + matched = False + # todo: display failed hunk, i.e. expected/found + + fp.close() + return matched + + + def patch_stream(self, instream, hunks): + """ Generator that yields stream patched with hunks iterable + + Converts lineends in hunk lines to the best suitable format + autodetected from input + """ + + # todo: At the moment substituted lineends may not be the same + # at the start and at the end of patching. Also issue a + # warning/throw about mixed lineends (is it really needed?) + + hunks = iter(hunks) + + srclineno = 1 + + lineends = {'\n':0, '\r\n':0, '\r':0} + def get_line(): + """ + local utility function - return line from source stream + collecting line end statistics on the way + """ + line = instream.readline() + # 'U' mode works only with text files + if line.endswith("\r\n"): + lineends["\r\n"] += 1 + elif line.endswith("\n"): + lineends["\n"] += 1 + elif line.endswith("\r"): + lineends["\r"] += 1 + return line + + for hno, h in enumerate(hunks): + debug("hunk %d" % (hno+1)) + if h.hasminus: + warning("Change removes/replaces some text; INVESTIGATE AND APPLY (OR NOT) MANUALLY") + warning("Change:") + changeText = h.originalText() + if len(changeText) > 1000: + changeText = changeText[0:999] + "...\n" + warning(changeText) + else: + # skip to line just before hunk starts + while srclineno < h.startsrc: + yield get_line() + srclineno += 1 + + for hline in h.text: + # todo: check \ No newline at the end of file + if hline.startswith("-") or hline.startswith("\\"): + get_line() + srclineno += 1 + continue + else: + if not hline.startswith("+"): + get_line() + srclineno += 1 + line2write = hline[1:] + # detect if line ends are consistent in source file + if sum([bool(lineends[x]) for x in lineends]) == 1: + newline = [x for x in lineends if lineends[x] != 0][0] + yield line2write.rstrip("\r\n")+newline + else: # newlines are mixed + yield line2write + + for line in instream: + yield line + + + def write_hunks(self, srcname, tgtname, hunks): + src = open(srcname, "rb") + tgt = open(tgtname, "wb") + + debug("processing target file %s" % tgtname) + + tgt.writelines(self.patch_stream(src, hunks)) + + tgt.close() + src.close() + # [ ] TODO: add test for permission copy + shutil.copymode(srcname, tgtname) + return True + + + +if __name__ == "__main__": + from optparse import OptionParser + from os.path import exists + import sys + + opt = OptionParser(usage="1. %prog [options] unified.diff\n" + " 2. %prog [options] http://host/patch\n" + " 3. %prog [options] -- < unified.diff", + version="python-patch %s" % __version__) + opt.add_option("-q", "--quiet", action="store_const", dest="verbosity", + const=0, help="print only warnings and errors", default=1) + opt.add_option("-v", "--verbose", action="store_const", dest="verbosity", + const=2, help="be verbose") + opt.add_option("--debug", action="store_true", dest="debugmode", help="debug mode") + opt.add_option("--diffstat", action="store_true", dest="diffstat", + help="print diffstat and exit") + opt.add_option("-p", "--strip", type="int", metavar='N', default=0, + help="strip N path components from filenames") + (options, args) = opt.parse_args() + + if not args and sys.argv[-1:] != ['--']: + opt.print_version() + opt.print_help() + sys.exit() + readstdin = (sys.argv[-1:] == ['--'] and not args) + + debugmode = options.debugmode + + verbosity_levels = {0:logging.WARNING, 1:logging.INFO, 2:logging.DEBUG} + loglevel = verbosity_levels[options.verbosity] + logformat = "%(message)s" + if debugmode: + loglevel = logging.DEBUG + logformat = "%(levelname)8s %(message)s" + logger.setLevel(loglevel) + loghandler = logging.StreamHandler() + loghandler.setFormatter(logging.Formatter(logformat)) + logger.addHandler(loghandler) + + + if readstdin: + patch = PatchSet(sys.stdin) + else: + patchfile = args[0] + urltest = patchfile.split(':')[0] + if (':' in patchfile and urltest.isalpha() + and len(urltest) > 1): # one char before : is a windows drive letter + patch = fromurl(patchfile) + else: + if not exists(patchfile) or not isfile(patchfile): + sys.exit("patch file does not exist - %s" % patchfile) + patch = fromfile(patchfile) + + if options.diffstat: + print patch.diffstat() + sys.exit(0) + + #pprint(patch) + patch.apply(options.strip) or sys.exit(-1) + + # todo: document and test line ends handling logic - patch.py detects proper line-endings + # for inserted hunks and issues a warning if patched file has incosistent line ends diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.jobs.rst --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -48,6 +48,7 @@ galaxy.jobs.actions galaxy.jobs.deferred + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.jobs.runners.rst --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -57,14 +57,6 @@ :undoc-members: :show-inheritance: -:mod:`sge` Module ------------------ - -.. automodule:: galaxy.jobs.runners.sge - :members: - :undoc-members: - :show-inheritance: - :mod:`tasks` Module ------------------- diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.tool_shed.rst --- a/doc/source/lib/galaxy.tool_shed.rst +++ b/doc/source/lib/galaxy.tool_shed.rst @@ -9,6 +9,14 @@ :undoc-members: :show-inheritance: +:mod:`common_util` Module +------------------------- + +.. automodule:: galaxy.tool_shed.common_util + :members: + :undoc-members: + :show-inheritance: + :mod:`encoding_util` Module --------------------------- diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.util.rst --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -25,6 +25,14 @@ :undoc-members: :show-inheritance: +:mod:`debugging` Module +----------------------- + +.. automodule:: galaxy.util.debugging + :members: + :undoc-members: + :show-inheritance: + :mod:`expressions` Module ------------------------- @@ -113,6 +121,14 @@ :undoc-members: :show-inheritance: +:mod:`shed_util_common` Module +------------------------------ + +.. automodule:: galaxy.util.shed_util_common + :members: + :undoc-members: + :show-inheritance: + :mod:`streamball` Module ------------------------ diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.webapps.community.rst --- a/doc/source/lib/galaxy.webapps.community.rst +++ b/doc/source/lib/galaxy.webapps.community.rst @@ -42,4 +42,5 @@ galaxy.webapps.community.framework galaxy.webapps.community.model galaxy.webapps.community.security + galaxy.webapps.community.util diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.webapps.community.util.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.util.rst @@ -0,0 +1,27 @@ +util Package +============ + +:mod:`container_util` Module +---------------------------- + +.. automodule:: galaxy.webapps.community.util.container_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`hgweb_config` Module +-------------------------- + +.. automodule:: galaxy.webapps.community.util.hgweb_config + :members: + :undoc-members: + :show-inheritance: + +:mod:`shed_statistics` Module +----------------------------- + +.. automodule:: galaxy.webapps.community.util.shed_statistics + :members: + :undoc-members: + :show-inheritance: + diff -r de8bc5bde938c937759ced066ef28ce1f6202641 -r eae248415389203907b5b951f139a200024ae069 doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -293,6 +293,14 @@ :undoc-members: :show-inheritance: +:mod:`item_tags` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.item_tags + :members: + :undoc-members: + :show-inheritance: + :mod:`libraries` Module ----------------------- 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: 3 new changesets
by Bitbucket 18 Dec '12

18 Dec '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/da270e660db5/ changeset: da270e660db5 user: natefoo date: 2012-12-18 21:41:10 summary: Backed out changeset 0d6653d29222, this needs to go to -dist so it will be committed on the current dist parent and then merged back to -central. affected #: 1 file diff -r 0d6653d29222880e3ade27bd055569ccebc7234e -r da270e660db5594d14205ac7a2dfd8f3b0fcc649 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1511,7 +1511,6 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): - message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) metadata = tool_shed_repository.metadata @@ -1552,14 +1551,14 @@ tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: - message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ + message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ % ( tool_shed_repository.name, original_section_name ) message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " - message += "different section in the tool panel. " + message += "different section in the tool panel." status = 'warning' else: - message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name - message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " + message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name + message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section." status = 'warning' if metadata and 'readme_files' in metadata: url = suc.url_join( tool_shed_url, @@ -1583,9 +1582,9 @@ install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: - if tool_shed_repository.includes_tool_dependencies: - message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " - message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. " + if includes_tool_dependencies: + message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " + message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository." status = "warning" install_tool_dependencies_check_box_checked = False else: https://bitbucket.org/galaxy/galaxy-central/changeset/cda19f585a15/ changeset: cda19f585a15 user: natefoo date: 2012-12-18 21:41:41 summary: From Dave B.: Fix for reinstalling repository with tool dependencies when tool_dependency_dir is not set. affected #: 1 file diff -r 140b1d164818a3ecba581b9e313a1b846f120164 -r cda19f585a15241a1ee91a795a995a8f1dcca188 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1511,6 +1511,7 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): + message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) metadata = tool_shed_repository.metadata @@ -1551,14 +1552,14 @@ tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ % ( tool_shed_repository.name, original_section_name ) message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " - message += "different section in the tool panel." + message += "different section in the tool panel. " status = 'warning' else: - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name - message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section." + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name + message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' if metadata and 'readme_files' in metadata: url = suc.url_join( tool_shed_url, @@ -1582,9 +1583,9 @@ install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: - if includes_tool_dependencies: - message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " - message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository." + if tool_shed_repository.includes_tool_dependencies: + message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " + message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. " status = "warning" install_tool_dependencies_check_box_checked = False else: https://bitbucket.org/galaxy/galaxy-central/changeset/de8bc5bde938/ changeset: de8bc5bde938 user: natefoo date: 2012-12-18 21:42:24 summary: Merged changes from galaxy-dist-staging. affected #: 1 file diff -r da270e660db5594d14205ac7a2dfd8f3b0fcc649 -r de8bc5bde938c937759ced066ef28ce1f6202641 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1511,6 +1511,7 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): + message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) metadata = tool_shed_repository.metadata @@ -1551,14 +1552,14 @@ tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ % ( tool_shed_repository.name, original_section_name ) message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " - message += "different section in the tool panel." + message += "different section in the tool panel. " status = 'warning' else: - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name - message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section." + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name + message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' if metadata and 'readme_files' in metadata: url = suc.url_join( tool_shed_url, @@ -1582,9 +1583,9 @@ install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: - if includes_tool_dependencies: - message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " - message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository." + if tool_shed_repository.includes_tool_dependencies: + message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " + message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. " status = "warning" install_tool_dependencies_check_box_checked = False else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Fix for reinstalling repository with tool dependencies when tool_dependency_dir is not set.
by Bitbucket 18 Dec '12

18 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0d6653d29222/ changeset: 0d6653d29222 user: inithello date: 2012-12-18 21:31:46 summary: Fix for reinstalling repository with tool dependencies when tool_dependency_dir is not set. affected #: 1 file diff -r 829ee499d6953c1b6efb957d93918b4d3f3ac1a4 -r 0d6653d29222880e3ade27bd055569ccebc7234e lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1511,6 +1511,7 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): + message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) metadata = tool_shed_repository.metadata @@ -1551,14 +1552,14 @@ tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ % ( tool_shed_repository.name, original_section_name ) message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " - message += "different section in the tool panel." + message += "different section in the tool panel. " status = 'warning' else: - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name - message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section." + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name + message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' if metadata and 'readme_files' in metadata: url = suc.url_join( tool_shed_url, @@ -1582,9 +1583,9 @@ install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: - if includes_tool_dependencies: - message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " - message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository." + if tool_shed_repository.includes_tool_dependencies: + message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " + message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. " status = "warning" install_tool_dependencies_check_box_checked = False else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 18 Dec '12

18 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/140b1d164818/ changeset: 140b1d164818 user: carlfeberhard date: 2012-12-18 20:51:26 summary: pack scripts affected #: 2 files diff -r 454638eb2434c827350b2c8dadbc04760ffa11b6 -r 140b1d164818a3ecba581b9e313a1b846f120164 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 @@ -var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>')},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(){},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(){},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 454638eb2434c827350b2c8dadbc04760ffa11b6 -r 140b1d164818a3ecba581b9e313a1b846f120164 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/829ee499d695/ changeset: 829ee499d695 user: carlfeberhard date: 2012-12-18 21:02:46 summary: merge staging:140b1d164818 to central affected #: 2 files diff -r 9ff8e6f3b0813fa3acbc76f94ad6a9d426d4752b -r 829ee499d6953c1b6efb957d93918b4d3f3ac1a4 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 @@ -var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>')},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(){},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(){},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 9ff8e6f3b0813fa3acbc76f94ad6a9d426d4752b -r 829ee499d6953c1b6efb957d93918b4d3f3ac1a4 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ 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: inithello: Fix for installing tool shed repository when tool_dependency_dir is not set. Toll shed functional test enhancements.
by Bitbucket 18 Dec '12

18 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9ff8e6f3b081/ changeset: 9ff8e6f3b081 user: inithello date: 2012-12-18 20:48:14 summary: Fix for installing tool shed repository when tool_dependency_dir is not set. Toll shed functional test enhancements. affected #: 5 files diff -r eb39627264622db4805927d0d0f35972067a58b7 -r 9ff8e6f3b0813fa3acbc76f94ad6a9d426d4752b lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -44,7 +44,11 @@ dependency_name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] - install_dir = os.path.join( trans.app.config.tool_dependency_dir, + if trans.app.config.tool_dependency_dir: + root_dir = trans.app.config.tool_dependency_dir + else: + root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>' + install_dir = os.path.join( root_dir, dependency_name, version, repository_owner, diff -r eb39627264622db4805927d0d0f35972067a58b7 -r 9ff8e6f3b0813fa3acbc76f94ad6a9d426d4752b templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -47,7 +47,7 @@ ${render_readme_section( containers_dict )} <div style="clear: both"></div> %endif - %if includes_repository_dependencies or ( includes_tool_dependencies and trans.app.config.use_tool_dependencies ): + %if includes_repository_dependencies or includes_tool_dependencies: <div class="form-row"><table class="colored" width="100%"><th bgcolor="#EBD9B2">Confirm dependency installation</th> diff -r eb39627264622db4805927d0d0f35972067a58b7 -r 9ff8e6f3b0813fa3acbc76f94ad6a9d426d4752b test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -28,6 +28,8 @@ self.file_dir = os.environ.get( 'TOOL_SHED_TEST_FILE_DIR', None ) self.tool_shed_test_file = None self.tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' ) + # TODO: Figure out a way to alter these attributes during tests. + self.galaxy_tool_dependency_dir = None # os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} self.home() def browse_category( self, category, strings_displayed=[], strings_not_displayed=[] ): @@ -387,12 +389,12 @@ tc.fv( "3", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def install_repository( self, name, owner, category_name, install_tool_dependencies=False, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): + def install_repository( self, name, owner, category_name, install_tool_dependencies=False, changeset_revision=None, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[] ): if test_db_util.get_installed_repository_by_name_owner( name, owner ) is not None: return self.browse_tool_shed( url=self.url ) self.browse_category( test_db_util.get_category_by_name( category_name ) ) - self.preview_repository_in_tool_shed( name, common.test_user_1_name, strings_displayed=[] ) + self.preview_repository_in_tool_shed( name, common.test_user_1_name, strings_displayed=preview_strings_displayed ) repository = test_db_util.get_repository_by_name_and_owner( name, owner ) repository_id = self.security.encode_id( repository.id ) if changeset_revision is None: @@ -402,10 +404,13 @@ self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) if 'install_tool_dependencies' in self.last_page(): + form = tc.browser.get_form( 'select_tool_panel_section' ) + checkbox = form.find_control( id="install_tool_dependencies" ) + checkbox.disabled = False if install_tool_dependencies: - tc.fv( '1', 'install_tool_dependencies', True ) + checkbox.selected = True else: - tc.fv( '1', 'install_tool_dependencies', False ) + checkbox.selected = False tc.submit( 'select_tool_panel_section_button' ) html = self.last_page() # Since the installation process is by necessity asynchronous, we have to get the parameters to 'manually' initiate the diff -r eb39627264622db4805927d0d0f35972067a58b7 -r 9ff8e6f3b0813fa3acbc76f94ad6a9d426d4752b test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -62,10 +62,15 @@ self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0010 Repository With Tool Dependencies' ] ) category = test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' ) self.browse_category( category, strings_displayed=[ 'freebayes_0010' ] ) - self.preview_repository_in_tool_shed( 'freebayes_0010', common.test_user_1_name, strings_displayed=[ 'freebayes_0010', 'Valid tools' ] ) + self.preview_repository_in_tool_shed( 'freebayes_0010', common.test_user_1_name, strings_displayed=[ 'freebayes_0010', 'Valid tools', 'Tool dependencies' ] ) def test_0015_install_freebayes_repository( self ): '''Install the freebayes repository without installing tool dependencies.''' - self.install_repository( 'freebayes_0010', common.test_user_1_name, 'Test 0010 Repository With Tool Dependencies', install_tool_dependencies=False ) + strings_displayed=[ 'set your tool_dependency_dir', 'can be automatically installed', 'Set the tool_dependency_dir' ] + self.install_repository( 'freebayes_0010', + common.test_user_1_name, + 'Test 0010 Repository With Tool Dependencies', + strings_displayed=strings_displayed, + install_tool_dependencies=False ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) self.verify_installed_repository_on_browse_page( installed_repository ) self.display_installed_repository_manage_page( installed_repository, diff -r eb39627264622db4805927d0d0f35972067a58b7 -r 9ff8e6f3b0813fa3acbc76f94ad6a9d426d4752b test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -140,6 +140,7 @@ new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_shed_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + os.environ[ 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir if 'TOOL_SHED_TEST_DBURI' in os.environ: toolshed_database_connection = os.environ[ 'TOOL_SHED_TEST_DBURI' ] else: @@ -268,7 +269,6 @@ file_path = galaxy_file_path, tool_path = tool_path, tool_data_path = tool_data_path, - tool_dependency_dir=galaxy_tool_dependency_dir, shed_tool_path=galaxy_shed_tool_path, update_integrated_tool_panel = False, tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 18 Dec '12

18 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/454638eb2434/ changeset: 454638eb2434 user: carlfeberhard date: 2012-12-18 19:53:55 summary: history panel: fix to js behaviors on late-rendered hda bodies affected #: 2 files diff -r c961f5647673a8cbe5f0f7275b82513e2067afc9 -r 454638eb2434c827350b2c8dadbc04760ffa11b6 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -78,16 +78,12 @@ itemWrapper.append( this._render_warnings() ); itemWrapper.append( this._render_titleBar() ); + //NOTE: only sets behaviors on title and warnings - body will set up it's own + this._setUpBehaviors( itemWrapper ); + this.body = $( this._render_body() ); itemWrapper.append( this.body ); - //TODO: move to own function: setUpBehaviours - // we can potentially skip this step and call popupmenu directly on the download button - make_popup_menus( itemWrapper ); - - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); - // transition... this.$el.fadeOut( 'fast', function(){ view.$el.children().remove(); @@ -155,6 +151,17 @@ }); }, + /** set up js behaviors, event handlers for elements within the given container + * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) + */ + _setUpBehaviors : function( $container ){ + $container = $container || this.$el; + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) + //TODO: we can potentially skip this step and call popupmenu directly on the download button + make_popup_menus( $container ); + $container.find( '.tooltip' ).tooltip({ placement : 'bottom' }); + }, + // ................................................................................ RENDER titlebar /** Render any hda warnings including: is deleted, is purged, is hidden. * (including links to further actions (undelete, etc.)) @@ -389,6 +396,7 @@ body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) ); } body.append( '<div style="clear: both"></div>' ); + this._setUpBehaviors( body ); }, /** Render inaccessible, not-owned by curr user. diff -r c961f5647673a8cbe5f0f7275b82513e2067afc9 -r 454638eb2434c827350b2c8dadbc04760ffa11b6 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -220,7 +220,15 @@ * @returns array of encoded ids */ ids : function(){ - return this.map( function( item ){ return item.id; }); + return this.map( function( hda ){ return hda.id; }); + }, + + /** Get the hda with the given hid + * @param {Int} hid the hid to search for + * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found + */ + getByHid : function( hid ){ + return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); }, /** If the given hid is in the collection, return it's index. If not, return the insertion point it would need. https://bitbucket.org/galaxy/galaxy-central/changeset/eb3962726462/ changeset: eb3962726462 user: carlfeberhard date: 2012-12-18 20:37:54 summary: merge staging:454638eb2434 to central affected #: 2 files diff -r 715063d652abc9dc3197617012763284143e7ab2 -r eb39627264622db4805927d0d0f35972067a58b7 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -78,16 +78,12 @@ itemWrapper.append( this._render_warnings() ); itemWrapper.append( this._render_titleBar() ); + //NOTE: only sets behaviors on title and warnings - body will set up it's own + this._setUpBehaviors( itemWrapper ); + this.body = $( this._render_body() ); itemWrapper.append( this.body ); - //TODO: move to own function: setUpBehaviours - // we can potentially skip this step and call popupmenu directly on the download button - make_popup_menus( itemWrapper ); - - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); - // transition... this.$el.fadeOut( 'fast', function(){ view.$el.children().remove(); @@ -155,6 +151,17 @@ }); }, + /** set up js behaviors, event handlers for elements within the given container + * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) + */ + _setUpBehaviors : function( $container ){ + $container = $container || this.$el; + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) + //TODO: we can potentially skip this step and call popupmenu directly on the download button + make_popup_menus( $container ); + $container.find( '.tooltip' ).tooltip({ placement : 'bottom' }); + }, + // ................................................................................ RENDER titlebar /** Render any hda warnings including: is deleted, is purged, is hidden. * (including links to further actions (undelete, etc.)) @@ -389,6 +396,7 @@ body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) ); } body.append( '<div style="clear: both"></div>' ); + this._setUpBehaviors( body ); }, /** Render inaccessible, not-owned by curr user. diff -r 715063d652abc9dc3197617012763284143e7ab2 -r eb39627264622db4805927d0d0f35972067a58b7 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -220,7 +220,15 @@ * @returns array of encoded ids */ ids : function(){ - return this.map( function( item ){ return item.id; }); + return this.map( function( hda ){ return hda.id; }); + }, + + /** Get the hda with the given hid + * @param {Int} hid the hid to search for + * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found + */ + getByHid : function( hid ){ + return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); }, /** If the given hid is in the collection, return it's index. If not, return the insertion point it would need. 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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