[galaxy-commits] commit/galaxy-central: greg: Fixes for installing tool shed repositories.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3301ed8fea42/ changeset: 3301ed8fea42 user: greg date: 2012-12-12 20:35:12 summary: Fixes for installing tool shed repositories. affected #: 8 files diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -636,9 +636,6 @@ relative_install_dir = os.path.join( tool_path, partial_install_dir ) return tool_path, relative_install_dir return None, None -def get_tool_shed_from_clone_url( repository_clone_url ): - tmp_url = clean_repository_clone_url( repository_clone_url ) - return tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) 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 @@ -693,18 +690,6 @@ changeset_revision = None ctx_rev = None return changeset_revision, ctx_rev -def get_url_from_repository_tool_shed( app, repository ): - """ - The stored value of repository.tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is - something like: http://toolshed.g2.bx.psu.edu/. - """ - for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): - if shed_url.find( repository.tool_shed ) >= 0: - if shed_url.endswith( '/' ): - shed_url = shed_url.rstrip( '/' ) - return shed_url - # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. - return None def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ): """ Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1,4 +1,4 @@ -import os, shutil, tempfile, logging, string, threading +import os, shutil, tempfile, logging, string, threading, urllib2 from galaxy import util from galaxy.tools import parameters from galaxy.util import inflector @@ -91,12 +91,12 @@ folder_id, readme_files_root_folder = build_readme_files_folder( folder_id, readme_files_dict ) containers_dict[ 'readme_files' ] = readme_files_root_folder if repository_dependencies: - folder_id, repository_dependencies_root_folder = 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 ) + 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 if tool_dependencies: folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) @@ -526,42 +526,44 @@ trans.sa_session.add( repository_metadata ) trans.sa_session.flush() return repository_metadata -def create_repo_info_dict( trans, repo, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, - repository=None, repository_metadata=None ): +def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, repository=None, + repository_metadata=None, metadata=None, repository_dependencies=None ): """ - Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance. The dictionary will also contain - the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. This method is called during the - tool shed repository installation process from Galaxy. In this case both the received repository and repository_metadata will be objects, but repository_name - sill be None. This method is also called when a tool shed repository that was uninstalled from a Galaxy instance is being re-installed. In this case, both - repository and repository_metadata will be None, but repository_name will have a value. + Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance. The dictionary will also + contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. + + This method is called from Galaxy from two places: + 1. During the tool shed repository installation process (via the tool shed's get_repository_information() method)- in this case both the received + repository and repository_metadata will be objects. + 2. When a tool shed repository that was uninstalled from a Galaxy instance is being re-installed - in this case, both repository and + repository_metadata will be None, but metadata will be the tool_shed_repository metadata on the Galaxy side, and the repository_dependencies will + be an object previously retrieved from the tool shed. """ repo_info_dict = {} - if repository is None and repository_metadata is None: - # The repository associated with the received repository_clone_url is being re-installed into a Galaxy instance, so we need to retrieve the - # appropriate repository from the tool shed using the received information. - repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + if trans.webapp.name == 'community': + # We're in the tool shed. repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - # Get a dictionary of all repositories upon which the contents of the received repository depends. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, - repo=repo, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None, - circular_repository_dependencies=None ) - # Cast unicode to string. - repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), - str( repository_clone_url ), - str( changeset_revision ), - str( ctx_rev ), - str( repository_owner ), - repository_dependencies, - metadata.get( 'tool_dependencies', None ) ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + # Get a dictionary of all repositories upon which the contents of the received repository depends. + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None, + circular_repository_dependencies=None ) + # Cast unicode to string. + repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), + str( repository_clone_url ), + str( changeset_revision ), + str( ctx_rev ), + str( repository_owner ), + repository_dependencies, + metadata.get( 'tool_dependencies', None ) ) return repo_info_dict def generate_clone_url_for_repository_in_tool_shed( trans, repository ): """Generate the URL for cloning a repository that is in the tool shed.""" @@ -1189,12 +1191,18 @@ return valid_filenames def get_repository_by_name_and_owner( trans, name, owner ): """Get a repository from the database via name and owner""" + if trans.webapp.name == 'galaxy': + return trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( and_( trans.model.ToolShedRepository.table.c.name == name, + trans.model.ToolShedRepository.table.c.owner == owner ) ) \ + .first() + # We're in the tool shed. user = get_user_by_username( trans, owner ) return trans.sa_session.query( trans.model.Repository ) \ .filter( and_( trans.model.Repository.table.c.name == name, trans.model.Repository.table.c.user_id == user.id ) ) \ .first() -def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, +def get_repository_dependencies_for_changeset_revision( trans, repository, repository_metadata, toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ): """ @@ -1291,7 +1299,7 @@ """Get a repository on the tool shed side from the database via id""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): - """Get metadata for a specified repository change set from the database""" + """Get metadata for a specified repository change set from the database.""" # Make sure there are no duplicate records, and return the single unique record for the changeset_revision. Duplicate records were somehow # created in the past. The cause of this issue has been resolved, but we'll leave this method as is for a while longer to ensure all duplicate # records are removed. @@ -1357,6 +1365,9 @@ relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths +def get_tool_shed_from_clone_url( repository_clone_url ): + tmp_url = clean_repository_clone_url( repository_clone_url ) + return tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ): updated_key_rd_dicts = [] for key_rd_dict in key_rd_dicts: @@ -1387,6 +1398,18 @@ # We have the updated changset revision. updated_key_rd_dicts.append( new_key_rd_dict ) return updated_key_rd_dicts +def get_url_from_repository_tool_shed( app, repository ): + """ + The stored value of repository.tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is + something like: http://toolshed.g2.bx.psu.edu/. + """ + for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): + if shed_url.find( repository.tool_shed ) >= 0: + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + return shed_url + # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. + return None def get_user_by_username( trans, username ): """Get a user from the database by username""" return trans.sa_session.query( trans.model.User ) \ @@ -1412,7 +1435,7 @@ new_key_rd_dict[ current_repository_key ] = rd_copy current_repository_key_rd_dicts.append( new_key_rd_dict ) if current_repository_key_rd_dicts: - toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ + toolshed, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ handle_key_rd_dicts_for_repository( trans, current_repository_key, current_repository_key_rd_dicts, @@ -1420,7 +1443,6 @@ handled_key_rd_dicts, circular_repository_dependencies ) return get_repository_dependencies_for_changeset_revision( trans=trans, - repo=required_repo, repository=required_repository, repository_metadata=required_repository_metadata, toolshed_base_url=toolshed, @@ -1456,8 +1478,6 @@ trans.security.encode_id( required_repository.id ), changeset_revision ) if required_repository_metadata: - required_repo_dir = required_repository.repo_path( trans.app ) - required_repo = hg.repository( get_configured_ui(), required_repo_dir ) # The required_repository_metadata changeset_revision is installable. required_metadata = required_repository_metadata.metadata if required_metadata: @@ -1475,12 +1495,12 @@ error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " error_message += "for tool shed %s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision ) log.debug( error_message ) - return toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts + return toolshed, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts def handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ): next_repository_key_rd_dict = key_rd_dicts_to_be_processed.pop( 0 ) next_repository_key_rd_dicts = [ next_repository_key_rd_dict ] next_repository_key = next_repository_key_rd_dict.keys()[ 0 ] - toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ + toolshed, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ handle_key_rd_dicts_for_repository( trans, next_repository_key, next_repository_key_rd_dicts, @@ -1488,7 +1508,6 @@ handled_key_rd_dicts, circular_repository_dependencies ) return get_repository_dependencies_for_changeset_revision( trans=trans, - repo=required_repo, repository=required_repository, repository_metadata=required_repository_metadata, toolshed_base_url=toolshed, diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1243,6 +1243,58 @@ message=message, status=status ) @web.expose + def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): + """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + galaxy_url = kwd.get( 'galaxy_url', '' ) + name = params.get( 'name', None ) + owner = params.get( 'owner', None ) + changeset_revision = params.get( 'changeset_revision', None ) + repository = get_repository_by_name_and_owner( trans, name, owner ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + # Default to the received changeset revision and ctx_rev. + update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) + ctx_rev = str( update_to_ctx.rev() ) + latest_changeset_revision = changeset_revision + update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev ) + if changeset_revision == repository.tip( trans.app ): + # If changeset_revision is the repository tip, there are no additional updates. + return tool_shed_encode( update_dict ) + else: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. + return tool_shed_encode( update_dict ) + else: + # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the + # repository was installed. We need to find the changeset_revision to which we need to update. + update_to_changeset_hash = None + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + ctx = get_changectx_for_changeset( repo, changeset_hash ) + if update_to_changeset_hash: + if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): + # We found a RepositoryMetadata record. + if changeset_hash == repository.tip( trans.app ): + # The current ctx is the repository tip, so use it. + update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) + latest_changeset_revision = changeset_hash + else: + update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash ) + latest_changeset_revision = update_to_changeset_hash + break + elif not update_to_changeset_hash and changeset_hash == changeset_revision: + # We've found the changeset in the changelog for which we need to get the next update. + update_to_changeset_hash = changeset_hash + update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) + update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) + return tool_shed_encode( update_dict ) + @web.expose def get_ctx_rev( self, trans, **kwd ): """Given a repository and changeset_revision, return the correct ctx.rev() value.""" repository_name = kwd[ 'name' ] @@ -1274,6 +1326,30 @@ return repository_metadata.metadata return None @web.json + def get_repository_dependencies( self, trans, **kwd ): + params = util.Params( kwd ) + name = params.get( 'name', None ) + owner = params.get( 'owner', None ) + changeset_revision = params.get( 'changeset_revision', None ) + repository = get_repository_by_name_and_owner( trans, name, owner ) + repository_id = trans.security.encode_id( repository.id ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + # Get a dictionary of all repositories upon which the contents of the received repository depends. + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None, + circular_repository_dependencies=None ) + if repository_dependencies: + return tool_shed_encode( repository_dependencies ) + return '' + @web.json def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ): """ Generate a list of dictionaries, each of which contains the information about a repository that will be necessary for installing @@ -1299,13 +1375,13 @@ repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = create_repo_info_dict( trans=trans, - repo=repo, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, ctx_rev=str( ctx.rev() ), repository_owner=repository.user.username, - repository_name=None, + repository_name=repository.name, repository=repository, + metadata=None, repository_metadata=repository_metadata ) repo_info_dicts.append( tool_shed_encode( repo_info_dict ) ) return dict( includes_tools=includes_tools, @@ -1370,58 +1446,6 @@ if tool_version_dicts: return to_json_string( tool_version_dicts ) return '' - @web.expose - def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): - """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', '' ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) - repository = get_repository_by_name_and_owner( trans, name, owner ) - repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( get_configured_ui(), repo_dir ) - # Default to the received changeset revision and ctx_rev. - update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) - ctx_rev = str( update_to_ctx.rev() ) - latest_changeset_revision = changeset_revision - update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev ) - if changeset_revision == repository.tip( trans.app ): - # If changeset_revision is the repository tip, there are no additional updates. - return tool_shed_encode( update_dict ) - else: - repository_metadata = get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: - # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. - return tool_shed_encode( update_dict ) - else: - # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the - # repository was installed. We need to find the changeset_revision to which we need to update. - update_to_changeset_hash = None - for changeset in repo.changelog: - changeset_hash = str( repo.changectx( changeset ) ) - ctx = get_changectx_for_changeset( repo, changeset_hash ) - if update_to_changeset_hash: - if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): - # We found a RepositoryMetadata record. - if changeset_hash == repository.tip( trans.app ): - # The current ctx is the repository tip, so use it. - update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) - latest_changeset_revision = changeset_hash - else: - update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash ) - latest_changeset_revision = update_to_changeset_hash - break - elif not update_to_changeset_hash and changeset_hash == changeset_revision: - # We've found the changeset in the changelog for which we need to get the next update. - update_to_changeset_hash = changeset_hash - update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) - update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) - return tool_shed_encode( update_dict ) def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions.""" encoded_id = trans.security.encode_id( repository.id ) @@ -1783,7 +1807,6 @@ if repository_metadata: # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, - repo=repo, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), @@ -1896,7 +1919,6 @@ metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, - repo=repo, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), @@ -2418,7 +2440,6 @@ metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, - repo=repo, repository=repository, repository_metadata=repository_metadata, toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 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 @@ -561,6 +561,28 @@ trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' return get_repository_file_contents( file_path ) + @web.expose + @web.require_admin + def get_repository_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): + """ + Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined for the received repository + name, owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We + need it so that we can derive the tool shed from which it was installed. + """ + repository = get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) + url = url_join( tool_shed_url, + 'repository/get_repository_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ + ( repository_name, repository_owner, changeset_revision ) ) + response = urllib2.urlopen( url ) + raw_text = response.read() + response.close() + if len( raw_text ) > 2: + text = json.from_json_string( tool_shed_decode( raw_text ) ) + log.debug( text ) + else: + text = '' + return text def get_versions_of_tool( self, app, guid ): tool_version = get_tool_version( app, guid ) return tool_version.get_version_ids( app, reverse=True ) @@ -1348,17 +1370,24 @@ repo_info_dict = kwd.get( 'repo_info_dict', None ) # The repo_info_dict should be encoded. if not repo_info_dict: - # This should only happen if the tool_shed_repository does not include any valid tools. + # Entering this if block used to happen only if the tool_shed_repository does not include any valid tools. After repository dependencies + # were introduced, it may never happen, but will keep the block just in case. + repository_dependencies = self.get_repository_dependencies( trans=trans, + repository_id=repository_id, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + changeset_revision=tool_shed_repository.installed_changeset_revision ) repo = hg.repository( get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) ) repo_info_dict = create_repo_info_dict( trans=trans, - repo=repo, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.installed_changeset_revision, ctx_rev=ctx_rev, repository_owner=tool_shed_repository.owner, repository_name=tool_shed_repository.name, repository=None, - repository_metadata=None ) + repository_metadata=None, + metadata=metadata, + repository_dependencies=repository_dependencies ) repo_info_dict = tool_shed_encode( repo_info_dict ) new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, @@ -1434,21 +1463,27 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): - repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) - metadata = repository.metadata - tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - ctx_rev = get_ctx_rev( tool_shed_url, repository.name, repository.owner, repository.installed_changeset_revision ) - repository_clone_url = generate_clone_url_for_installed_repository( trans, repository ) - repo = hg.repository( get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) ) + repository_id = kwd[ 'id' ] + tool_shed_repository = get_installed_tool_shed_repository( trans, repository_id ) + metadata = tool_shed_repository.metadata + tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + ctx_rev = get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) + repository_clone_url = generate_clone_url_for_installed_repository( trans, tool_shed_repository ) + repository_dependencies = self.get_repository_dependencies( trans=trans, + repository_id=repository_id, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + changeset_revision=tool_shed_repository.installed_changeset_revision ) repo_info_dict = create_repo_info_dict( trans=trans, - repo=repo, repository_clone_url=repository_clone_url, - changeset_revision=repository.installed_changeset_revision, + changeset_revision=tool_shed_repository.installed_changeset_revision, ctx_rev=ctx_rev, - repository_owner=repository.owner, - repository_name=repository.name, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, repository=None, - repository_metadata=None ) + repository_metadata=None, + metadata=metadata, + repository_dependencies=repository_dependencies ) # Get the location in the tool panel in which the tool was originally loaded. if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] @@ -1469,18 +1504,18 @@ no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ - % ( repository.name, original_section_name ) + % ( tool_shed_repository.name, original_section_name ) message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " message += "different section in the tool panel." status = 'warning' else: - message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % repository.name + message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section." status = 'warning' if metadata and 'readme_files' in metadata: url = url_join( tool_shed_url, 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \ - ( repository.name, repository.owner, repository.installed_changeset_revision ) ) + ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() response.close() @@ -1508,7 +1543,7 @@ install_tool_dependencies_check_box_checked = True install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako', - repository=repository, + repository=tool_shed_repository, no_changes_check_box=no_changes_check_box, original_section_name=original_section_name, install_repository_dependencies_check_box=install_repository_dependencies_check_box, diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -159,7 +159,7 @@ def __str__( self ): return str( self.count ) - readme_files_root_folder = containers_dict[ 'readme_files' ] + readme_files_root_folder = containers_dict.get( 'readme_files', None ) %> %if readme_files_root_folder: <p/> diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -11,7 +11,7 @@ <div class="toolFormBody"><form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='reinstall_repository', id=trans.security.encode_id( repository.id ), repo_info_dict=encoded_repo_info_dict )}" method="post" ><div style="clear: both"></div> - <% readme_files_dict = containers_dict[ 'readme_files' ] %> + <% readme_files_dict = containers_dict.get( 'readme_files', None ) %> %if readme_files_dict: <div class="form-row"><table class="colored" width="100%"> diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -37,7 +37,7 @@ <div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div> - <% readme_files_dict = containers_dict[ 'readme_files' ] %> + <% readme_files_dict = containers_dict.get( 'readme_files', None ) %> %if readme_files_dict: <div class="form-row"><table class="colored" width="100%"> diff -r c8c181a904677adf0c9c65a1151848d9d2da16fb -r 3301ed8fea42b1067f88138573b7d716c3b631e5 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -467,13 +467,13 @@ has_readme_files = metadata and 'readme_files' in metadata has_workflows = metadata and 'workflows' in metadata - datatypes_root_folder = containers_dict[ 'datatypes' ] - invalid_tools_root_folder = containers_dict[ 'invalid_tools' ] - readme_files_root_folder = containers_dict[ 'readme_files' ] - repository_dependencies_root_folder = containers_dict[ 'repository_dependencies' ] - tool_dependencies_root_folder = containers_dict[ 'tool_dependencies' ] - valid_tools_root_folder = containers_dict[ 'valid_tools' ] - workflows_root_folder = containers_dict[ 'workflows' ] + datatypes_root_folder = containers_dict.get( 'datatypes', None ) + invalid_tools_root_folder = containers_dict.get( 'invalid_tools', None ) + readme_files_root_folder = containers_dict.get( 'readme_files', None ) + repository_dependencies_root_folder = containers_dict.get( 'repository_dependencies', None ) + tool_dependencies_root_folder = containers_dict.get( 'tool_dependencies', None ) + valid_tools_root_folder = containers_dict.get( 'valid_tools', none ) + workflows_root_folder = containers_dict.get( 'workflows', None ) has_contents = datatypes_root_folder or invalid_tools_root_folder or valid_tools_root_folder or workflows_root_folder Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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