galaxy-commits December 2012

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commit/galaxy-central: greg: Various fixes and enhancements to support new repository dependencies.
by Bitbucket 05 Dec '12

05 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6304eb6a9110/ changeset: 6304eb6a9110 user: greg date: 2012-12-05 16:47:48 summary: Various fixes and enhancements to support new repository dependencies. affected #: 5 files diff -r 5c5249fac5c8893a8da13043b8cc1ba23d3b303e -r 6304eb6a91103121ed6d6bf960b6bc9984966259 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 +79,11 @@ 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 ) + tool_dependencies = add_installation_directories_to_tool_dependencies( trans, + repository_name, + repository_owner, + changeset_revision, + tool_dependencies ) try: folder_id = 0 if readme_files_dict: @@ -321,6 +325,7 @@ log.debug( error_message ) return False, error_message def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): + """Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created.""" # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of # current_changeset_revision which is associated with current_metadata_dict. A new repository_metadata record will be created only # when this method returns the string 'not equal and not subset'. @@ -328,23 +333,38 @@ ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ] ancestor_guids.sort() + ancestor_repository_dependencies_dict = ancestor_metadata_dict.get( 'repository_dependencies', {} ) + ancestor_repository_dependencies = ancestor_repository_dependencies_dict.get( 'repository_dependencies', [] ) ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', [] ) ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) current_datatypes = current_metadata_dict.get( 'datatypes', [] ) current_tools = current_metadata_dict.get( 'tools', [] ) current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] current_guids.sort() + current_repository_dependencies_dict = current_metadata_dict.get( 'repository_dependencies', {} ) + current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] ) current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', [] ) current_workflows = current_metadata_dict.get( 'workflows', [] ) # Handle case where no metadata exists for either changeset. - if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes: + no_datatypes = not ancestor_datatypes and not current_datatypes + no_repository_dependencies = not ancestor_repository_dependencies and not current_repository_dependencies + # Note: we currently don't need to check tool_dependencies since we're checking for guids - tool_dependencies always require tools (currently). + no_tool_dependencies = not ancestor_tool_dependencies and not current_tool_dependencies + no_tools = not ancestor_guids and not current_guids + no_workflows = not ancestor_workflows and not current_workflows + if no_datatypes and no_repository_dependencies and no_tool_dependencies and no_tools and no_workflows: return 'no metadata' + repository_dependency_comparison = compare_repository_dependencies( ancestor_repository_dependencies, current_repository_dependencies ) workflow_comparison = compare_workflows( ancestor_workflows, current_workflows ) datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) # Handle case where all metadata is the same. - if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': + if ancestor_guids == current_guids and repository_dependency_comparison == 'equal' and workflow_comparison == 'equal' and datatype_comparison == 'equal': return 'equal' - if workflow_comparison in [ 'equal', 'subset' ] and datatype_comparison in [ 'equal', 'subset' ]: + # Handle case where ancestor metadata is a subset of current metadata. + repository_dependency_is_subset = repository_dependency_comparison in [ 'equal', 'subset' ] + workflow_dependency_is_subset = workflow_comparison in [ 'equal', 'subset' ] + datatype_is_subset = datatype_comparison in [ 'equal', 'subset' ] + if repository_dependency_is_subset and workflow_dependency_is_subset and datatype_is_subset: is_subset = True for guid in ancestor_guids: if guid not in current_guids: @@ -354,10 +374,8 @@ return 'subset' return 'not equal and not subset' def compare_datatypes( ancestor_datatypes, current_datatypes ): - # Determine if ancestor_datatypes is the same as current_datatypes - # or if ancestor_datatypes is a subset of current_datatypes. Each - # datatype dict looks something like: - # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} + """Determine if ancestor_datatypes is the same as or a subset of current_datatypes.""" + # Each datatype dict looks something like: {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} if len( ancestor_datatypes ) <= len( current_datatypes ): for ancestor_datatype in ancestor_datatypes: # Currently the only way to differentiate datatypes is by name. @@ -378,9 +396,31 @@ else: return 'subset' return 'not equal and not subset' +def compare_repository_dependencies( ancestor_repository_dependencies, current_repository_dependencies ): + """Determine if ancestor_repository_dependencies is the same as or a subset of current_repository_dependencies.""" + # The list of repository_dependencies looks something like: [["http://localhost:9009", "emboss_datatypes", "test", "ab03a2a5f407"]]. + # Create a string from each tuple in the list for easier comparison. + if len( ancestor_repository_dependencies ) <= len( current_repository_dependencies ): + for ancestor_tup in ancestor_repository_dependencies: + ancestor_tool_shed, ancestor_repository_name, ancestor_repository_owner, ancestor_changeset_revision = ancestor_tup + found_in_current = False + for current_tup in current_repository_dependencies: + current_tool_shed, current_repository_name, current_repository_owner, current_changeset_revision = current_tup + if current_tool_shed == ancestor_tool_shed and \ + current_repository_name == ancestor_repository_name and \ + current_repository_owner == ancestor_repository_owner and \ + current_changeset_revision == ancestor_changeset_revision: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_repository_dependencies ) == len( current_repository_dependencies ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' def compare_workflows( ancestor_workflows, current_workflows ): - # Determine if ancestor_workflows is the same as current_workflows - # or if ancestor_workflows is a subset of current_workflows. + """Determine if ancestor_workflows is the same as current_workflows or if ancestor_workflows is a subset of current_workflows.""" if len( ancestor_workflows ) <= len( current_workflows ): for ancestor_workflow_tup in ancestor_workflows: # ancestor_workflows is a list of tuples where each contained tuple is @@ -417,6 +457,7 @@ message = '' return message def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ): + """Copy all files currently on disk that end with the .sample extension to the directory to which dest_path refers.""" sample_files = [] for root, dirs, files in os.walk( repo_files_dir ): if root.find( '.hg' ) < 0: @@ -664,10 +705,12 @@ # If the list of sample files includes a tool_data_table_conf.xml.sample file, laad it's table elements into memory. relative_path, filename = os.path.split( sample_file ) if filename == 'tool_data_table_conf.xml.sample': - new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=sample_file, - tool_data_path=original_tool_data_path, - shed_tool_data_table_config=app.config.shed_tool_data_table_config, - persist=persist ) + new_table_elems, error_message = app.tool_data_tables.add_new_entries_from_config_file( config_filename=sample_file, + tool_data_path=original_tool_data_path, + shed_tool_data_table_config=app.config.shed_tool_data_table_config, + persist=persist ) + if error_message: + invalid_file_tups.append( ( filename, error_message ) ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -675,13 +718,8 @@ for name in files: # See if we have a repository dependencies defined. if name == 'repository_dependencies.xml': - relative_path_to_repository_dependencies = get_relative_path_to_repository_file( root, - name, - relative_install_dir, - work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) - metadata_dict = generate_repository_dependency_metadata( relative_path_to_repository_dependencies, metadata_dict ) + path_to_repository_dependencies_config = os.path.join( root, name ) + metadata_dict = generate_repository_dependency_metadata( path_to_repository_dependencies_config, metadata_dict ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = get_relative_path_to_repository_file( root, @@ -793,7 +831,9 @@ if repository_dependencies_tup not in repository_dependencies_tups: repository_dependencies_tups.append( repository_dependencies_tup ) if repository_dependencies_tups: - metadata_dict[ 'repository_dependencies' ] = repository_dependencies_tups + repository_dependencies_dict = dict( description=root.get( 'description' ), + repository_dependencies=repository_dependencies_tups ) + metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict return metadata_dict def generate_tool_dependency_metadata( app, repository, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ @@ -1087,25 +1127,47 @@ 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, repository_dependencies=None, - all_repository_dependencies=None ): + all_repository_dependencies=None, handled=None ): """ Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend. The dictionary keys are name-spaced values consisting of toolshed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of repository_dependency tuples consisting of ( toolshed_base_url, repository_name, repository_owner, changeset_revision ). This method ensures that all required repositories to the nth degree are returned. """ + if handled is None: + handled = [] if all_repository_dependencies is None: all_repository_dependencies = {} if repository_dependencies is None: repository_dependencies = [] metadata = repository_metadata.metadata if metadata and 'repository_dependencies' in metadata: + repository_dependencies_dict = metadata[ 'repository_dependencies' ] + # The repository_dependencies entry in the metadata is a dictionary that may have a value for a 'description' key. We want to + # store the value of this key only once, the first time through this recursive method. repository_dependencies_root_key = generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, repository_name=repository.name, repository_owner=repository.user.username, changeset_revision=repository_metadata.changeset_revision ) - for repository_dependency in metadata[ 'repository_dependencies' ]: - if repository_dependency not in repository_dependencies: + if not all_repository_dependencies: + # Initialize the all_repository_dependencies dictionary. + all_repository_dependencies[ 'root_key' ] = repository_dependencies_root_key + all_repository_dependencies[ repository_dependencies_root_key ] = [] + if 'description' not in all_repository_dependencies: + description = repository_dependencies_dict.get( 'description', None ) + all_repository_dependencies[ 'description' ] = description + + # The next key of interest in repository_dependencies_dict is 'repository_dependencies', which is a list of tuples. + repository_dependencies_tups = repository_dependencies_dict[ 'repository_dependencies' ] + for repository_dependency in repository_dependencies_tups: + # Skip repository dependencies that point to the root repository. + check_key = generate_repository_dependencies_key_for_repository( toolshed_base_url=repository_dependency[ 0 ], + repository_name=repository_dependency[ 1 ], + repository_owner=repository_dependency[ 2 ], + changeset_revision=repository_dependency[ 3 ] ) + if check_key == repository_dependencies_root_key: + handled.append( repository_dependency ) + elif repository_dependency not in handled and repository_dependency not in repository_dependencies: repository_dependencies.append( repository_dependency ) else: repository_dependencies_root_key = None @@ -1121,6 +1183,7 @@ if repository_dependency not in all_repository_dependencies_val: all_repository_dependencies_val.append( repository_dependency ) all_repository_dependencies[ repository_dependencies_root_key ] = all_repository_dependencies_val + handled.append( repository_dependency ) else: # Insert this repository_dependency. all_repository_dependencies[ repository_dependencies_root_key ] = [ repository_dependency ] @@ -1141,6 +1204,23 @@ required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( required_repository.id ), required_changeset_revision ) + if required_repository_metadata: + # The changeset_revision defined in a repository_dependencies.xml file is outdated, so we need to fix appropriate + # entries in our all_repository_dependencies dictionary. + updated_repository_dependency = [ tool_shed, name, owner, required_changeset_revision ] + for k, v in all_repository_dependencies.items(): + if k in [ 'root_key', 'description' ]: + continue + for i, current_repository_dependency in enumerate( v ): + current_tool_shed, current_name, current_owner, current_changeset_revision = current_repository_dependency + if tool_shed == current_tool_shed and name == current_name and owner == current_owner and changeset_revision == current_changeset_revision: + if updated_repository_dependency in v: + # We've already stored the updated repository_dependency, so remove the outdated one. + v = v.remove( repository_dependency ) + else: + # Store the updated repository_dependency. + v[ i ] = updated_repository_dependency + all_repository_dependencies[ k ] = v if required_repository_metadata: # The required_repository_metadata changeset_revision is installable. required_metadata = required_repository_metadata.metadata @@ -1151,7 +1231,8 @@ repository_metadata=required_repository_metadata, toolshed_base_url=tool_shed, repository_dependencies=repository_dependencies, - all_repository_dependencies=all_repository_dependencies ) + all_repository_dependencies=all_repository_dependencies, + handled=handled ) else: # The repository is in a different tool shed, so build an url and send a request. raise Exception( "Repository dependencies that refer to repositories in other tool sheds is not yet supported." ) @@ -1321,16 +1402,18 @@ error = False message = '' try: - new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=filename, - tool_data_path=app.config.tool_data_path, - shed_tool_data_table_config=app.config.shed_tool_data_table_config, - persist=persist ) + new_table_elems, message = app.tool_data_tables.add_new_entries_from_config_file( config_filename=filename, + tool_data_path=app.config.tool_data_path, + shed_tool_data_table_config=app.config.shed_tool_data_table_config, + persist=persist ) + if message: + error = True except Exception, e: message = str( e ) error = True return error, message def is_downloadable( metadata_dict ): - return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict + return 'datatypes' in metadata_dict or 'repository_dependencies' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_tool_from_config( app, full_path ): try: tool = app.toolbox.load_tool( full_path ) @@ -1502,14 +1585,15 @@ cloned_ok, error_message = clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - persist=False ) + current_metadata_dict, invalid_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + repository_clone_url=repository_clone_url, + relative_install_dir=repo_dir, + repository_files_dir=work_dir, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) + invalid_file_tups.extend( invalid_tups ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. @@ -1707,11 +1791,7 @@ if new_dependency_name and new_dependency_type and new_dependency_version: # Update all attributes of the tool_dependency record in the database. log.debug( "Updating tool dependency '%s' with type '%s' and version '%s' to have new type '%s' and version '%s'." % \ - ( str( tool_dependency.name ), - str( tool_dependency.type ), - str( tool_dependency.version ), - str( new_dependency_type ), - str( new_dependency_version ) ) ) + ( str( tool_dependency.name ), str( tool_dependency.type ), str( tool_dependency.version ), str( new_dependency_type ), str( new_dependency_version ) ) ) tool_dependency.type = new_dependency_type tool_dependency.version = new_dependency_version tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED diff -r 5c5249fac5c8893a8da13043b8cc1ba23d3b303e -r 6304eb6a91103121ed6d6bf960b6bc9984966259 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -191,17 +191,13 @@ tool.id, tool.version ) def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): + stripped_file_name = strip_path( file_name ) file_path = None - found = False for root, dirs, files in os.walk( repo_files_dir ): if root.find( '.hg' ) < 0: for name in files: - if name == file_name: - file_path = os.path.abspath( os.path.join( root, name ) ) - found = True - break - if found: - break + if name == stripped_file_name: + return os.path.abspath( os.path.join( root, name ) ) return file_path def get_category( trans, id ): """Get a category from the database""" @@ -501,7 +497,6 @@ as_html=True, displaying_invalid_tool=True ) message = concat_messages( message, message2 ) - status = 'error' else: tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) remove_dir( work_dir ) diff -r 5c5249fac5c8893a8da13043b8cc1ba23d3b303e -r 6304eb6a91103121ed6d6bf960b6bc9984966259 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1019,6 +1019,8 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository, tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + if message: + status = 'error' tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) @@ -1760,7 +1762,7 @@ repository_metadata_id = None metadata = None is_malicious = False - repository_dependencies = [] + repository_dependencies = None if changeset_revision != INITIAL_CHANGELOG_HASH: repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -1786,7 +1788,8 @@ repository_metadata, str( url_for( '/', qualified=True ) ).rstrip( '/' ), repository_dependencies=None, - all_repository_dependencies=None ) + all_repository_dependencies=None, + handled=None ) if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push @@ -1898,7 +1901,8 @@ repository_metadata, str( url_for( '/', qualified=True ) ).rstrip( '/' ), repository_dependencies=None, - all_repository_dependencies=None ) + all_repository_dependencies=None, + handled=None ) else: repository_metadata_id = None metadata = None @@ -2383,7 +2387,7 @@ email_alerts = from_json_string( repository.email_alerts ) else: email_alerts = [] - repository_dependencies = [] + repository_dependencies = None user = trans.user if user and params.get( 'receive_email_alerts_button', False ): flush_needed = False @@ -2419,7 +2423,8 @@ repository_metadata, str( url_for( '/', qualified=True ) ).rstrip( '/' ), repository_dependencies=None, - all_repository_dependencies=None ) + all_repository_dependencies=None, + handled=None ) else: repository_metadata_id = None metadata = None diff -r 5c5249fac5c8893a8da13043b8cc1ba23d3b303e -r 6304eb6a91103121ed6d6bf960b6bc9984966259 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 @@ -11,6 +11,7 @@ self.id = id self.key = key self.label = label + self.description = None self.datatypes = [] self.folders = [] self.invalid_tools = [] @@ -24,7 +25,8 @@ if folder == contained_folder: return index, contained_folder return 0, None - + def remove_repository_dependency( self, repository_dependency ): + self.repository_dependencies.remove( repository_dependency ) class Datatype( object ): """Datatype object""" def __init__( self, id=None, extension=None, type=None, mimetype=None, subclass=None ): @@ -57,6 +59,9 @@ self.repository_name = repository_name self.repository_owner = repository_owner self.changeset_revision = changeset_revision + @property + def listify( self ): + return [ self.toolshed, self.repository_name, self.repository_owner, self.changeset_revision ] class Tool( object ): """Tool object""" @@ -183,11 +188,15 @@ repository_dependencies_root_folder = Folder( id=folder_id, key='root', label='root' ) folder_id += 1 # Create the Repository dependencies folder and add it to the root folder. - key = generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision ) - repository_dependencies_folder = Folder( id=folder_id, key=key, label=label ) + repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] + repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label ) + # The received repository_dependencies is a dictionary with a single 'description' key, and one or more repository_dependency keys. + # We want the description value associated with the repository_dependencies_folder. + repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) - # Process the repository dependencies. for key, val in repository_dependencies.items(): + if key in [ 'root_key', 'description' ]: + continue # Only create a new folder object if necessary. folder = get_folder( repository_dependencies_root_folder, key ) if not folder: @@ -197,19 +206,20 @@ folder = Folder( id=folder_id, key=key, label=label ) for repository_dependency_tup in val: toolshed, name, owner, changeset_revision = repository_dependency_tup - if not is_folder( repository_dependencies.keys(), toolshed, name, owner, changeset_revision ): - # Create a new repository_dependency. - repository_dependency_id += 1 - repository_dependency = RepositoryDependency( id=repository_dependency_id, - toolshed=toolshed, - repository_name=name, - repository_owner=owner, - changeset_revision=changeset_revision ) - # Insert the repository_dependency into the folder. - folder.repository_dependencies.append( repository_dependency ) + # Create a new repository_dependency. + repository_dependency_id += 1 + repository_dependency = RepositoryDependency( id=repository_dependency_id, + toolshed=toolshed, + repository_name=name, + repository_owner=owner, + changeset_revision=changeset_revision ) + # Insert the repository_dependency into the folder. + folder.repository_dependencies.append( repository_dependency ) if not get_folder( repository_dependencies_folder, key ): # Insert the folder into the list. repository_dependencies_folder.folders.append( folder ) + # Remove repository_dependencies that are also folders. + remove_unwanted_repository_dependencies( repository_dependencies_folder ) else: repository_dependencies_root_folder = None return folder_id, repository_dependencies_root_folder @@ -378,4 +388,10 @@ def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) return repository_name == key_name and repository_owner == key_owner and changeset_revision == key_changeset_revision +def remove_unwanted_repository_dependencies( folder ): + for repository_dependency in folder.repository_dependencies: + toolshed, name, owner, changeset_revision = repository_dependency.listify + key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) + if get_folder( folder, key ): + folder.remove_repository_dependency( repository_dependency ) \ No newline at end of file diff -r 5c5249fac5c8893a8da13043b8cc1ba23d3b303e -r 6304eb6a91103121ed6d6bf960b6bc9984966259 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -204,7 +204,10 @@ if folder.datatypes: col_span_str = 'colspan="4"' elif folder.label == 'Repository dependencies': - folder_label = "%s<i> - this repository requires installation of these additional repositories</i>" % folder_label + if folder.description: + folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) + else: + folder_label = "%s<i> - this repository requires installation of these additional repositories</i>" % folder_label elif folder.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: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Handle exceptions when parsing proprietary tool_data_table_conf.xml.sample files in the tool shed, and use the webapp's configured tool_data_path when configuring and loading the ToolDataTableManager.
by Bitbucket 05 Dec '12

05 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5c5249fac5c8/ changeset: 5c5249fac5c8 user: greg date: 2012-12-05 16:46:50 summary: Handle exceptions when parsing proprietary tool_data_table_conf.xml.sample files in the tool shed, and use the webapp's configured tool_data_path when configuring and loading the ToolDataTableManager. affected #: 1 file diff -r e40fdd5f6e8936f936f7118b0b9521f7379972ee -r 5c5249fac5c8893a8da13043b8cc1ba23d3b303e lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -77,8 +77,15 @@ </table> """ - tree = util.parse_xml( config_filename ) - root = tree.getroot() + error_message = '' + table_elems = [] + try: + tree = util.parse_xml( config_filename ) + root = tree.getroot() + except Exception, e: + error_message = 'Error attempting to parse file %s: %s' % ( str( os.path.split( config_filename )[ 1 ] ), str( e ) ) + log.debug( error_message ) + return table_elems, error_message # Make a copy of the current list of data_table_elem_names so we can persist later if changes to the config file are necessary. original_data_table_elem_names = [ name for name in self.data_table_elem_names ] if root.tag == 'tables': @@ -86,7 +93,6 @@ tool_data_path=tool_data_path, from_shed_config=True ) else: - table_elems = [] type = root.get( 'type', 'tabular' ) assert type in tool_data_table_types, "Unknown data table type '%s'" % type table_elems.append( root ) @@ -101,7 +107,7 @@ if persist and self.data_table_elem_names != original_data_table_elem_names: # Persist Galaxy's version of the changed tool_data_table_conf.xml file. self.to_xml_file( shed_tool_data_table_config ) - return table_elems + return table_elems, error_message def to_xml_file( self, shed_tool_data_table_config ): """Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.""" full_path = os.path.abspath( shed_tool_data_table_config ) @@ -146,8 +152,8 @@ def __init__( self, config_element, tool_data_path ): super( TabularToolDataTable, self ).__init__( config_element, tool_data_path ) - self.configure_and_load( config_element ) - def configure_and_load( self, config_element ): + self.configure_and_load( config_element, tool_data_path ) + def configure_and_load( self, config_element, tool_data_path ): """ Configure and load table from an XML element. """ @@ -157,9 +163,16 @@ self.parse_column_spec( config_element ) # Read every file all_rows = [] - found = False for file_element in config_element.findall( 'file' ): - filename = file_element.get( 'path' ) + found = False + if tool_data_path: + # We're loading a tool in the tool shed, so we cannot use the Galaxy tool-data + # directory which is hard-coded into the tool_data_table_conf.xml entries. + filepath = file_element.get( 'path' ) + filename = os.path.split( filepath )[ 1 ] + filename = os.path.join( tool_data_path, filename ) + else: + filename = file_element.get( 'path' ) if os.path.exists( filename ): found = True all_rows.extend( self.parse_file_fields( open( filename ) ) ) 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: base/_panels.mako: IE console protection; history panel: move hda updater into history-model (from HDACollection), handle new hdas more gracefully, handle hidden hdas that move into the ready states.
by Bitbucket 04 Dec '12

04 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e40fdd5f6e89/ changeset: e40fdd5f6e89 user: carlfeberhard date: 2012-12-04 20:43:49 summary: base/_panels.mako: IE console protection; history panel: move hda updater into history-model (from HDACollection), handle new hdas more gracefully, handle hidden hdas that move into the ready states. affected #: 8 files diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -72,7 +72,13 @@ if( urlKey === 'meta_download' ){ urls[ urlKey ] = hdaView._renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); } else { - urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); + try { + urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); + } catch( Error ){ + throw( hdaView + '._renderUrls error: ' + Error + + '\n rendering:' + urlTemplateOrObj + + '\n with ' + JSON.stringify( modelJson ) ); + } } } }); @@ -109,7 +115,6 @@ itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ), initialRender = ( this.$el.children().size() === 0 ); - //console.debug( this + '.render, initial?:', initialRender ); this.$el.attr( 'id', 'historyItemContainer-' + id ); itemWrapper @@ -362,7 +367,7 @@ break; default: //??: no body? - body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) ); + body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) ); } body.append( '<div style="clear: both"></div>' ); @@ -520,6 +525,11 @@ } }, + + remove : function(){ + + }, + // ......................................................................... MISC toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -193,7 +193,6 @@ if( !( this.model.hasData() ) || !( visualizations && visualizations.length ) || !( visualization_url ) ){ - //console.warn( 'NOT rendering visualization icon' ) this.visualizationsButton = null; return null; } diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -32,13 +32,14 @@ // ---whereas these are Dataset related/inherited id : null, - name : '', + name : '(unnamed dataset)', // one of HistoryDatasetAssociation.STATES - state : '', + state : 'ok', // sniffed datatype (sam, tabular, bed, etc.) data_type : null, // size in bytes file_size : 0, + file_ext : '', // array of associated file types (eg. [ 'bam_index', ... ]) meta_files : [], @@ -48,10 +49,10 @@ deleted : false, purged : false, - // aka. !hidden + // aka. !hidden (start hidden) visible : false, // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset )) - accessible : false + accessible : true }, /** fetch location of this history in the api */ @@ -59,6 +60,7 @@ url : function(){ //TODO: get this via url router return 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); + //TODO: this breaks on save() }, /** Set up the model, determine if accessible, bind listeners @@ -222,6 +224,34 @@ return this.map( function( item ){ return item.id; }); }, + /** If the given hid is in the collection, return it's index. If not, return the insertion point it would need. + * NOTE: assumes hids are unique and valid + * @param {Int} hid the hid to find or create. If hid is 0, null, undefined: return the last hid + 1 + * @returns the collection index of the existing hda or an insertion point if it doesn't exist + */ + hidToCollectionIndex : function( hid ){ + // if the hid is 0, null, undefined: assume a request for a new hid (return the last index) + if( !hid ){ + return this.models.length; + } + + var endingIndex = this.models.length - 1; + //TODO: prob. more efficient to cycle backwards through these (assuming ordered by hid) + for( var i=endingIndex; i>=0; i-- ){ + var hdaHid = this.at( i ).get( 'hid' ); + //this.log( i, 'hdaHid:', hdaHid ); + if( hdaHid == hid ){ + //this.log( '\t match:', hdaHid, hid, ' returning:', i ); + return i; + } + if( hdaHid < hid ){ + //this.log( '\t past it, returning:', ( i + 1 ) ); + return i + 1; + } + } + return null; + }, + /** Get every 'shown' hda in this collection based on show_deleted/hidden * @param {Boolean} show_deleted are we showing deleted hdas? * @param {Boolean} show_hidden are we showing hidden hdas? @@ -263,24 +293,31 @@ }, /** Update (fetch) the data of the hdas with the given ids. + * @param {String} historyId the id of the history containing this collection * @param {String[]} ids an array of hda ids to update + * @returns {HistoryDatasetAssociation[]} hda models that were updated * @see HistoryDatasetAssociation#fetch */ update : function( ids ){ this.log( this + 'update:', ids ); - if( !( ids && ids.length ) ){ return; } + if( !( ids && ids.length ) ){ return []; } - var collection = this; + var collection = this, + updatedHdas = null; _.each( ids, function( id, index ){ - var historyItem = collection.get( id ); - historyItem.fetch(); + var hda = collection.get( id ); + if( hda ){ + hda.fetch(); + updatedHdas.push( hda ); + } }); + return updatedHdas; }, /** String representation. */ toString : function(){ - return ( 'HDACollection(' + this.ids().join(',') + ')' ); + return ( 'HDACollection()' ); } }); diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -88,8 +88,6 @@ history.fetch() ).then( function( userResponse, historyResponse ){ - //console.warn( 'fetched user: ', userResponse[0] ); - //console.warn( 'fetched history: ', historyResponse[0] ); history.attributes.user = userResponse[0]; //? meh. history.trigger( 'loaded:user', userResponse[0] ); @@ -102,7 +100,6 @@ // reset the collection to the hdas returned })).success( function( hdas ){ - //console.warn( 'fetched hdas', hdas ); history.hdas.reset( hdas ); history.checkForUpdates(); @@ -167,7 +164,7 @@ // send the changed ids (if any) to dataset collection to have them fetch their own model changes if( changedIds.length ){ - history.hdas.update( changedIds ); + history.updateHdas( changedIds ); } // set up to keep pulling if this history in run/queue state @@ -176,7 +173,7 @@ || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ setTimeout( function(){ history.stateUpdater(); - }, 4000 ); + }, History.UPDATE_DELAY ); // otherwise, we're now in a 'ready' state (no hdas running) } else { @@ -187,14 +184,70 @@ // if not interruption by iframe reload //TODO: remove when iframes are removed if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){ - //if( console && console.warn ){ - // console.warn( 'Error getting history updates from the server:', xhr, status, error ); - //} alert( _l( 'Error getting history updates from the server.' ) + '\n' + error ); } }); }, + /** Update the models in the hdas collection that match the ids given by getting their data + * via the api/AJAX. If a model exists in the collection, set will be used with the new data. + * If it's not in the collection, addHdas will be used to create it. + * @param {String[]} hdaIds an array of the encoded ids of the hdas to get from the server. + */ + updateHdas : function( hdaIds ){ + //TODO:?? move to collection? still need proper url + var history = this; + jQuery.ajax({ + url : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }), + + error : function( xhr, status, error ){ + var msg = 'ERROR updating hdas from api history contents:'; + history.log( msg, hdaIds, xhr, status, error ); + alert( msg + hdaIds.join(',') ); + }, + + /** when the proper models for the requested ids are returned, + * either update existing or create new entries in the hdas collection + * @inner + */ + success : function( hdaDataList, status, xhr ){ + history.log( history + '.updateHdas, success:', hdaDataList, status, xhr ); + //TODO: compile new models to be added in one go + var hdasToAdd = []; + + _.each( hdaDataList, function( hdaData, index ){ + var existingModel = history.hdas.get( hdaData.id ); + // if this model exists already, update it + if( existingModel ){ + history.log( 'found existing model in list for id ' + hdaData.id + ', updating...:' ); + existingModel.set( hdaData ); + + // if this model is new and isn't in the hda collection, cache it to be created + } else { + history.log( 'NO existing model for id ' + hdaData.id + ', creating...:' ); + modelsToAdd.push( hdaData ); + } + }); + if( hdasToAdd.length ){ + history.addHdas( hdasToAdd ); + } + } + }); + }, + + /** Add multiple hda models to the hdas collection from an array of hda data. + */ + addHdas : function( hdaDataList ){ + //TODO: this is all probably easier if hdas is a relation + var history = this; + //TODO:?? what about hidden? deleted? + _.each( hdaDataList, function( hdaData, index ){ + var indexFromHid = history.hdas.hidToCollectionIndex( hdaData.hid ); + hdaData.history_id = history.get( 'id' ); + history.hdas.add( new HistoryDatasetAssociation( hdaData ), { at: indexFromHid }); + }); + }, + toString : function(){ var nameString = ( this.get( 'name' ) )? ( ',' + this.get( 'name' ) ) : ( '' ); @@ -202,6 +255,13 @@ } }); +//------------------------------------------------------------------------------ CLASS VARS +/** When the history has running hdas, + * this is the amount of time between update checks from the server + */ +History.UPDATE_DELAY = 4000; + + //============================================================================== /** @class A collection of histories (per user). * (stub) currently unused. diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -160,6 +160,20 @@ 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 ); + + // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, + // then: remove it from the collection if the panel is set to NOT show hidden datasets + this.model.hdas.bind( 'change:state', + function( hda, newState, changedList ){ + //TODO: magic string here - somehow use HDA.states + if( ( hda.inReadyState() ) + && ( !hda.get( 'visible' ) ) + && ( !this.storage.get( 'show_hidden' ) ) ){ + this.removeHda( hda ); + } + }, + this ); + //this.bind( 'all', function(){ // this.log( arguments ); //}, this ); @@ -178,6 +192,8 @@ * @see PersistantStorage */ _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){ + //this.log( '_setUpWebStorage, initiallyExpanded:', initiallyExpanded, + // 'show_deleted:', show_deleted, 'show_hidden', show_hidden ); // data that needs to be persistant over page refreshes // (note the key function which uses the history id as well) @@ -197,7 +213,6 @@ // get the show_deleted/hidden settings giving priority to values passed in, // using web storage otherwise - //this.log( 'show_deleted:', show_deleted, 'show_hidden', show_hidden ); // if the page has specifically requested show_deleted/hidden, these will be either true or false // (as opposed to undefined, null) - and we give priority to that setting if( ( show_deleted === true ) || ( show_deleted === false ) ){ @@ -218,18 +233,31 @@ * @param {HistoryDatasetAssociation} hda hda to add to the collection */ add : function( hda ){ - //console.debug( 'add.' + this, hda ); - //TODO + //this.log( 'add.' + this, hda ); + //KISS: just re-render the entire thing when adding + this.render(); }, /** Event hander to respond when hdas are reset */ addAll : function(){ - //console.debug( 'addAll.' + this ); + //this.log( 'addAll.' + this ); // re render when all hdas are reset this.render(); }, + /** Remove a view from the panel and the assoc. model from the collection + * @param {HistoryDataAssociation} the hda to remove + */ + removeHda : function( hdaModel, callback ){ + var hdaView = this.hdaViews[ hdaModel.get( 'id' ) ]; + hdaView.$el.fadeOut( 'fast', function(){ + hdaView.$el.remove(); + if( callback ){ callback(); } + }); + this.model.hdas.remove( hdaModel ); + }, + // ......................................................................... RENDERING /** Render urls, historyPanel body, and hdas (if any are shown) * @see Backbone.View#render @@ -243,8 +271,6 @@ modelJson = this.model.toJSON(), initialRender = ( this.$el.children().size() === 0 ); - //console.debug( this + '.render, initialRender:', initialRender ); - // render the urls and add them to the model json modelJson.urls = this._renderUrls( modelJson ); @@ -466,7 +492,7 @@ } return false; }, - + // ......................................................................... MISC /** Return a string rep of the history */ diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -23,29 +23,39 @@ ## Default javascripts <%def name="javascripts()"> - ##  - - ${h.js( - "libs/jquery/jquery", - "libs/json2", - "libs/bootstrap", - "galaxy.base", - "libs/underscore", - "libs/backbone/backbone", - "libs/backbone/backbone-relational", - "libs/handlebars.runtime", - "mvc/ui" - )} - - <script type="text/javascript"> - // Set up needed paths. - var galaxy_paths = new GalaxyPaths({ - root_path: '${h.url_for( "/" )}', - image_path: '${h.url_for( "/static/images" )}' - }); - </script> + ##  + + ${h.js( + "libs/jquery/jquery", + "libs/json2", + "libs/bootstrap", + "galaxy.base", + "libs/underscore", + "libs/backbone/backbone", + "libs/backbone/backbone-relational", + "libs/handlebars.runtime", + "mvc/ui" + )} + + <script type="text/javascript"> + // console protection + window.console = window.console || { + log : function(){}, + debug : function(){}, + info : function(){}, + warn : function(){}, + error : function(){}, + assert : function(){}, + }; + + // Set up needed paths. + var galaxy_paths = new GalaxyPaths({ + root_path: '${h.url_for( "/" )}', + image_path: '${h.url_for( "/static/images" )}' + }); + </script></%def> ## Additional metas can be defined by templates inheriting from this one. diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -60,6 +60,16 @@ 'galaxy.base' )} <script type="text/javascript"> + // console protection + window.console = window.console || { + log : function(){}, + debug : function(){}, + info : function(){}, + warn : function(){}, + error : function(){}, + assert : function(){}, + }; + // Set up needed paths. var galaxy_paths = new GalaxyPaths({ root_path: '${h.url_for( "/" )}', diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -297,14 +297,13 @@ // add needed controller urls to GalaxyPaths galaxy_paths.set( 'hda', ${get_hda_url_templates()} ); galaxy_paths.set( 'history', ${get_history_url_templates()} ); -//console.debug( 'galaxy_paths:', galaxy_paths ); $(function(){ galaxyPageSetUp(); Galaxy.historyFrame = window; // ostensibly, this is the App - //if( console && console.debug ){ + //if( window.console && console.debug ){ // //if( console.clear ){ console.clear(); } // console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); } // top.storage = jQuery.jStorage @@ -315,9 +314,6 @@ var user = ${ get_current_user() }, history = ${ get_history( history.id ) }, hdas = ${ get_hdas( history.id, datasets ) }; - //console.debug( 'user:', user ); - //console.debug( 'history:', history ); - //console.debug( 'hdas:', hdas ); var currUser = new User( user ); if( !Galaxy.currUser ){ Galaxy.currUser = currUser; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Clean up imports in datasets controller.
by Bitbucket 04 Dec '12

04 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b175274d13e0/ changeset: b175274d13e0 user: jgoecks date: 2012-12-04 20:27:50 summary: Clean up imports in datasets controller. affected #: 1 file diff -r 87c8970719b135a7b2c9804484dc0d96df171083 -r b175274d13e0be88c4504d51aa0f49d0802cc42b lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -2,15 +2,8 @@ API operations on the contents of a dataset. """ import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * -from galaxy.visualization.data_providers.genome import * -from galaxy.visualization.data_providers.basic import ColumnDataProvider -from galaxy.datatypes.tabular import Vcf -from galaxy.model import NoConverterException, ConverterDependencyException +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, get_highest_priority_msg, messages from galaxy.web.framework.helpers import is_true log = logging.getLogger( __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: 2 new changesets
by Bitbucket 04 Dec '12

04 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b724301b1244/ changeset: b724301b1244 user: jgoecks date: 2012-12-04 20:15:08 summary: Remove import *'s from page controller. affected #: 1 file diff -r 3a1f833d3463ff3b5fc82eeff5adc72f1a07c6a9 -r b724301b1244c4c48e1e98336680b5eafce1c2c5 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -1,6 +1,8 @@ -from galaxy import model -from galaxy.model.item_attrs import * -from galaxy.web.base.controller import * +from sqlalchemy import desc +from galaxy import model, web +from galaxy.web import error, url_for +from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings +from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesHistoryMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor from galaxy.util.odict import odict https://bitbucket.org/galaxy/galaxy-central/changeset/87c8970719b1/ changeset: 87c8970719b1 user: jgoecks date: 2012-12-04 20:15:52 summary: merge affected #: 1 file diff -r b724301b1244c4c48e1e98336680b5eafce1c2c5 -r 87c8970719b135a7b2c9804484dc0d96df171083 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -4,15 +4,16 @@ """ import pkg_resources pkg_resources.require( "bx-python" ) - +import gzip import logging -import data +import os +from cgi import escape from galaxy import util -from cgi import escape +from galaxy.datatypes import data from galaxy.datatypes import metadata +from galaxy.datatypes.checkers import is_gzip from galaxy.datatypes.metadata import MetadataElement -import galaxy_utils.sequence.vcf -from sniff import * +from galaxy.datatypes.sniff import get_headers from galaxy.util.json import to_json_string log = logging.getLogger(__name__) @@ -264,10 +265,21 @@ return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1}) def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None): - #TODO Prevent failure when displaying extremely long > 50kb lines. if chunk: return self.get_chunk(trans, dataset, chunk) - if to_ext or not preview: + elif dataset.metadata.columns > 50: + #Fancy tabular display is only suitable for datasets without an incredibly large number of columns. + #We should add a new datatype 'matrix', with it's own draw method, suitable for this kind of data. + #For now, default to the old behavior, ugly as it is. Remove this after adding 'matrix'. + max_peek_size = 1000000 # 1 MB + if not preview or os.stat( dataset.file_name ).st_size < max_peek_size: + return open( dataset.file_name ) + else: + trans.response.set_content_type( "text/html" ) + return trans.stream_template_mako( "/dataset/large_file.mako", + truncated_data = open( dataset.file_name ).read(max_peek_size), + data = dataset) + elif to_ext or not preview: return self._serve_raw(trans, dataset, to_ext) else: column_names = 'null' @@ -589,7 +601,6 @@ - LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct - We will only check that up to the first 5 alignments are correctly formatted. """ - import gzip try: compress = is_gzip(filename) if compress: 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: dannon: Tabular Display: For extremely wide datasets, revert to the old behavior until we have a proper 'matrix' datatype w/ renderer. Cleanup/imports.
by Bitbucket 04 Dec '12

04 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bea6f76a652e/ changeset: bea6f76a652e user: dannon date: 2012-12-04 20:14:28 summary: Tabular Display: For extremely wide datasets, revert to the old behavior until we have a proper 'matrix' datatype w/ renderer. Cleanup/imports. affected #: 1 file diff -r 3a1f833d3463ff3b5fc82eeff5adc72f1a07c6a9 -r bea6f76a652e8f47e97c0995986bda8e939f714e lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -4,15 +4,16 @@ """ import pkg_resources pkg_resources.require( "bx-python" ) - +import gzip import logging -import data +import os +from cgi import escape from galaxy import util -from cgi import escape +from galaxy.datatypes import data from galaxy.datatypes import metadata +from galaxy.datatypes.checkers import is_gzip from galaxy.datatypes.metadata import MetadataElement -import galaxy_utils.sequence.vcf -from sniff import * +from galaxy.datatypes.sniff import get_headers from galaxy.util.json import to_json_string log = logging.getLogger(__name__) @@ -264,10 +265,21 @@ return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1}) def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None): - #TODO Prevent failure when displaying extremely long > 50kb lines. if chunk: return self.get_chunk(trans, dataset, chunk) - if to_ext or not preview: + elif dataset.metadata.columns > 50: + #Fancy tabular display is only suitable for datasets without an incredibly large number of columns. + #We should add a new datatype 'matrix', with it's own draw method, suitable for this kind of data. + #For now, default to the old behavior, ugly as it is. Remove this after adding 'matrix'. + max_peek_size = 1000000 # 1 MB + if not preview or os.stat( dataset.file_name ).st_size < max_peek_size: + return open( dataset.file_name ) + else: + trans.response.set_content_type( "text/html" ) + return trans.stream_template_mako( "/dataset/large_file.mako", + truncated_data = open( dataset.file_name ).read(max_peek_size), + data = dataset) + elif to_ext or not preview: return self._serve_raw(trans, dataset, to_ext) else: column_names = 'null' @@ -589,7 +601,6 @@ - LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct - We will only check that up to the first 5 alignments are correctly formatted. """ - import gzip try: compress = is_gzip(filename) if compress: 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: Make the HgWebConfigManager thread-safe.
by Bitbucket 04 Dec '12

04 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3a1f833d3463/ changeset: 3a1f833d3463 user: greg date: 2012-12-04 20:08:21 summary: Make the HgWebConfigManager thread-safe. affected #: 1 file diff -r 2635d1bcf9aab951981ddced7315cc0d4bf657b0 -r 3a1f833d3463ff3b5fc82eeff5adc72f1a07c6a9 lib/galaxy/webapps/community/util/hgweb_config.py --- a/lib/galaxy/webapps/community/util/hgweb_config.py +++ b/lib/galaxy/webapps/community/util/hgweb_config.py @@ -1,4 +1,4 @@ -import sys, os, ConfigParser, logging, shutil +import sys, os, ConfigParser, logging, shutil, threading from time import strftime from datetime import date @@ -15,32 +15,51 @@ self.in_memory_config = None def add_entry( self, lhs, rhs ): """Add an entry in the hgweb.config file for a new repository.""" - # Since we're changing the config, make sure the latest is loaded into memory. - self.read_config( force_read=True ) - # An entry looks something like: repos/test/mira_assembler = database/community_files/000/repo_123. - if rhs.startswith( './' ): - rhs = rhs.replace( './', '', 1 ) - self.make_backup() - # Add the new entry into memory. - self.in_memory_config.set( 'paths', lhs, rhs ) - # Persist our in-memory configuration. - self.write_config() + lock = threading.Lock() + lock.acquire( True ) + try: + # Since we're changing the config, make sure the latest is loaded into memory. + self.read_config( force_read=True ) + # An entry looks something like: repos/test/mira_assembler = database/community_files/000/repo_123. + if rhs.startswith( './' ): + rhs = rhs.replace( './', '', 1 ) + self.make_backup() + # Add the new entry into memory. + self.in_memory_config.set( 'paths', lhs, rhs ) + # Persist our in-memory configuration. + self.write_config() + except Exception, e: + log.debug( "Exception in HgWebConfigManager.add_entry(): %s" % str( e ) ) + finally: + lock.release() def change_entry( self, old_lhs, new_lhs, new_rhs ): """Change an entry in the hgweb.config file for a repository - this only happens when the owner changes the name of the repository.""" - self.make_backup() - # Remove the old entry. - self.in_memory_config.remove_option( 'paths', old_lhs ) - # Add the new entry. - self.in_memory_config.set( 'paths', new_lhs, new_rhs ) - # Persist our in-memory configuration. - self.write_config() + lock = threading.Lock() + lock.acquire( True ) + try: + self.make_backup() + # Remove the old entry. + self.in_memory_config.remove_option( 'paths', old_lhs ) + # Add the new entry. + self.in_memory_config.set( 'paths', new_lhs, new_rhs ) + # Persist our in-memory configuration. + self.write_config() + except Exception, e: + log.debug( "Exception in HgWebConfigManager.change_entry(): %s" % str( e ) ) + finally: + lock.release() def get_entry( self, lhs ): """Return an entry in the hgweb.config file for a repository""" self.read_config() try: entry = self.in_memory_config.get( 'paths', lhs ) except ConfigParser.NoOptionError: - raise Exception( "Entry for repository %s missing in file %s." % ( lhs, self.hgweb_config ) ) + try: + # We have a multi-threaded front-end, so one of the threads may not have the latest version of the hgweb.config file. + self.read_config( force_read=True ) + entry = self.in_memory_config.get( 'paths', lhs ) + except ConfigParser.NoOptionError: + raise Exception( "Entry for repository %s missing in file %s." % ( lhs, self.hgweb_config ) ) return entry @property def hgweb_config( self ): 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: jgoecks: Remove import *'s from visualization controller.
by Bitbucket 04 Dec '12

04 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2635d1bcf9aa/ changeset: 2635d1bcf9aa user: jgoecks date: 2012-12-04 20:05:30 summary: Remove import *'s from visualization controller. affected #: 1 file diff -r 1af9c4734df58bc3ff7cdca54733144cc8e6b9e2 -r 2635d1bcf9aab951981ddced7315cc0d4bf657b0 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -1,8 +1,9 @@ from __future__ import absolute_import -from galaxy import model -from galaxy.model.item_attrs import * -from galaxy.web.base.controller import * +from sqlalchemy import desc +from galaxy import model, web +from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings +from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin from galaxy.web.framework.helpers import time_ago, grids, iff from galaxy.util.sanitize_html import sanitize_html from galaxy.visualization.genomes import decode_dbkey 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: jgoecks: Fix output definition for GTF filter by attribute values list/
by Bitbucket 04 Dec '12

04 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1af9c4734df5/ changeset: 1af9c4734df5 user: jgoecks date: 2012-12-04 19:42:09 summary: Fix output definition for GTF filter by attribute values list/ affected #: 1 file diff -r ae3469a913214c4d5d5e6a1c5b449df978056972 -r 1af9c4734df58bc3ff7cdca54733144cc8e6b9e2 tools/filters/gff/gtf_filter_by_attribute_values_list.xml --- a/tools/filters/gff/gtf_filter_by_attribute_values_list.xml +++ b/tools/filters/gff/gtf_filter_by_attribute_values_list.xml @@ -14,7 +14,7 @@ <param format="tabular,txt" name="ids" type="data" label="And attribute values"/></inputs><outputs> - <data format="input" name="output" metadata_source="input"/> + <data format="gtf" name="output"/></outputs><tests> 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 04 Dec '12

04 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ebebacd0ccc4/ changeset: ebebacd0ccc4 user: jmchilton date: 2012-11-10 23:08:05 summary: Allow a datatype's merge method (used for parallelism) to take in an additional argument - the output_dataset object - if needed. No existing merge methods should need to be modified, the only modification to Galaxy's effective runtime behavior will occur if a datatype is defined which takes in a third keyword keyword argument called output_dataset. This change can enable the composite dataset parallelism pioneered by Jorrit Boekel, but one can imagine other potential uses (setting metadata derived from multiple files for instance). affected #: 1 file diff -r 5fdb5348d968f5bb38aedba23e26bdb9032a0c0b -r ebebacd0ccc45e5c0f26e0e7ceb55d70a0270dec lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -1,4 +1,5 @@ import os, logging, shutil +import inspect from galaxy import model, util @@ -125,7 +126,8 @@ output_file_name = str(outputs[output][1]) base_output_name = os.path.basename(output_file_name) if output in merge_outputs: - output_type = outputs[output][0].datatype + output_dataset = outputs[output][0] + output_type = output_dataset.datatype output_files = [os.path.join(dir,base_output_name) for dir in task_dirs] # Just include those files f in the output list for which the # file f exists; some files may not exist if a task fails. @@ -135,7 +137,13 @@ if len(output_files) < len(task_dirs): log.debug('merging only %i out of expected %i files for %s' % (len(output_files), len(task_dirs), output_file_name)) - output_type.merge(output_files, output_file_name) + # First two args to merge always output_files and path of dataset. More + # complicated merge methods may require more parameters. Set those up here. + extra_merge_arg_names = inspect.getargspec( output_type.merge ).args[2:] + extra_merge_args = {} + if "output_dataset" in extra_merge_arg_names: + extra_merge_args["output_dataset"] = output_dataset + output_type.merge(output_files, output_file_name, **extra_merge_args) log.debug('merge finished: %s' % output_file_name) else: msg = 'nothing to merge for %s (expected %i files)' \ https://bitbucket.org/galaxy/galaxy-central/changeset/ae3469a91321/ changeset: ae3469a91321 user: dannon date: 2012-12-04 15:45:52 summary: Merged in galaxyp/galaxy-central-optional-merge-args (pull request #83) affected #: 1 file diff -r 7bd130c33ebc218d97df83a63555abed222b301b -r ae3469a913214c4d5d5e6a1c5b449df978056972 lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -1,4 +1,5 @@ import os, logging, shutil +import inspect from galaxy import model, util @@ -125,7 +126,8 @@ output_file_name = str(outputs[output][1]) base_output_name = os.path.basename(output_file_name) if output in merge_outputs: - output_type = outputs[output][0].datatype + output_dataset = outputs[output][0] + output_type = output_dataset.datatype output_files = [os.path.join(dir,base_output_name) for dir in task_dirs] # Just include those files f in the output list for which the # file f exists; some files may not exist if a task fails. @@ -135,7 +137,13 @@ if len(output_files) < len(task_dirs): log.debug('merging only %i out of expected %i files for %s' % (len(output_files), len(task_dirs), output_file_name)) - output_type.merge(output_files, output_file_name) + # First two args to merge always output_files and path of dataset. More + # complicated merge methods may require more parameters. Set those up here. + extra_merge_arg_names = inspect.getargspec( output_type.merge ).args[2:] + extra_merge_args = {} + if "output_dataset" in extra_merge_arg_names: + extra_merge_args["output_dataset"] = output_dataset + output_type.merge(output_files, output_file_name, **extra_merge_args) log.debug('merge finished: %s' % output_file_name) else: msg = 'nothing to merge for %s (expected %i files)' \ 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