galaxy-commits December 2012

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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.

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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 19 Dec '12

19 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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galaxy-commits December 2012