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commit/galaxy-central: jgoecks: Unify system genome builds, custom builds, build len files, and build two bit files into a single python structure. Add function to get genome builds with or without build length information, and fix bugs so that the full build set (system + custom) is available via the API and when adding datasets to libraries.
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f36d5d615dd4/ changeset: f36d5d615dd4 user: jgoecks date: 2013-01-25 22:10:01 summary: Unify system genome builds, custom builds, build len files, and build two bit files into a single python structure. Add function to get genome builds with or without build length information, and fix bugs so that the full build set (system + custom) is available via the API and when adding datasets to libraries. affected #: 4 files diff -r 4a60baf34969dea43d30b4f18094dfd30c167b25 -r f36d5d615dd4775d71ee778f500bd0c1d3fdf68e lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -1,7 +1,7 @@ import os, re, sys, glob, logging from bx.seq.twobit import TwoBitFile from galaxy.util.json import from_json_string -from galaxy import model +from galaxy import model, util from galaxy.util.bunch import Bunch log = logging.getLogger( __name__ ) @@ -50,8 +50,9 @@ """ Encapsulates information about a known genome/dbkey. """ - def __init__( self, key, len_file=None, twobit_file=None ): + def __init__( self, key, description, len_file=None, twobit_file=None ): self.key = key + self.description = description self.len_file = len_file self.twobit_file = twobit_file @@ -160,16 +161,19 @@ """ def __init__( self, app ): - # Create list of known genomes from len files. + # Create list of genomes from util.dbnames self.genomes = {} + for key, description in util.dbnames: + self.genomes[ key ] = Genome( key, description ) + + # Add len files to genomes. len_files = glob.glob( os.path.join( app.config.len_file_path, "*.len" ) ) for f in len_files: key = os.path.split( f )[1].split( ".len" )[0] - self.genomes[ key ] = Genome( key, len_file=f ) + if key in self.genomes: + self.genomes[ key ].len_file = f # Add genome data (twobit files) to genomes. - # FIXME: If a galaxy instance does not have ~/tool-data/twobit.loc file, the following error is thrown: - # IOError: [Errno 2] No such file or directory: '~/tool-data/twobit.loc' try: for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ): if line.startswith("#"): continue @@ -179,6 +183,7 @@ if key in self.genomes: self.genomes[ key ].twobit_file = path except IOError, e: + # Thrown if twobit.loc does not exist. log.exception( str( e ) ) def get_build( self, dbkey ): @@ -188,17 +193,30 @@ rval = self.genomes[ dbkey ] return rval - def get_dbkeys_with_chrom_info( self, trans ): - """ Returns all valid dbkeys that have chromosome information. """ + def get_dbkeys( self, trans, chrom_info=False ): + """ Returns all known dbkeys. If chrom_info is True, only dbkeys with + chromosome lengths are returned. """ + dbkeys = [] - # All user keys have a len file. - user_keys = {} + # Add user's custom keys to dbkeys. + user_keys_dict = {} user = trans.get_user() if 'dbkeys' in user.preferences: - user_keys = from_json_string( user.preferences['dbkeys'] ) + user_keys_dict = from_json_string( user.preferences[ 'dbkeys' ] ) + dbkeys.extend( [ (attributes[ 'name' ], key ) for key, attributes in user_keys_dict.items() ] ) - dbkeys = [ (v, k) for k, v in trans.db_builds if ( ( k in self.genomes and self.genomes[ k ].len_file ) or k in user_keys ) ] + # Add app keys to dbkeys. + + # If chrom_info is True, only include keys with len files (which contain chromosome info). + filter_fn = lambda b: True + if chrom_info: + filter_fn = lambda b: b.len_file is not None + + dbkeys.extend( [ ( genome.description, genome.key ) for key, genome in self.genomes.items() if filter_fn( genome ) ] ) + return dbkeys + #return [ (v, k) for k, v in trans.db_builds if ( ( k in self.genomes and self.genomes[ k ].len_file ) or k in user_keys ) ] + def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ): """ @@ -224,6 +242,7 @@ user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) if dbkey in user_keys: dbkey_attributes = user_keys[ dbkey ] + dbkey_name = dbkey_attributes[ 'name' ] if 'fasta' in dbkey_attributes: build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] ) len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name @@ -234,7 +253,7 @@ elif 'len' in dbkey_attributes: len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name if len_file: - genome = Genome( dbkey, len_file=len_file, twobit_file=twobit_file ) + genome = Genome( dbkey, dbkey_name, len_file=len_file, twobit_file=twobit_file ) # Look in system builds. @@ -243,7 +262,7 @@ if not len_ds: genome = self.genomes[ dbkey ] else: - genome = Genome( dbkey, len_file=len_ds.file_name ) + genome = Genome( dbkey, dbkey_name, len_file=len_ds.file_name ) return genome.to_dict( num=num, chrom=chrom, low=low ) @@ -294,9 +313,9 @@ user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) dbkey_attributes = user_keys[ dbkey ] fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( dbkey_attributes[ 'fasta' ] ) - error = self._convert_dataset( trans, fasta_dataset, 'twobit' ) - if error: - return error + msg = fasta_dataset.convert_dataset( trans, 'twobit' ) + if msg: + return msg else: twobit_dataset = fasta_dataset.get_converted_dataset( trans, 'twobit' ) twobit_file_name = twobit_dataset.file_name @@ -309,31 +328,3 @@ return { 'dataset_type': 'refseq', 'data': seq_data } except IOError: return None - - ## FIXME: copied from tracks.py (tracks controller) - this should be consolidated when possible. - def _convert_dataset( self, trans, dataset, target_type ): - """ - Converts a dataset to the target_type and returns a message indicating - status of the conversion. None is returned to indicate that dataset - was converted successfully. - """ - - # Get converted dataset; this will start the conversion if necessary. - try: - converted_dataset = dataset.get_converted_dataset( trans, target_type ) - except NoConverterException: - return messages.NO_CONVERTER - except ConverterDependencyException, dep_error: - return { 'kind': messages.ERROR, 'message': dep_error.value } - - # Check dataset state and return any messages. - msg = None - if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: - job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ) \ - .filter_by( dataset_id=converted_dataset.id ).first().job_id - job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) - msg = { 'kind': messages.ERROR, 'message': job.stderr } - elif not converted_dataset or converted_dataset.state != model.Dataset.states.OK: - msg = messages.PENDING - - return msg \ No newline at end of file diff -r 4a60baf34969dea43d30b4f18094dfd30c167b25 -r f36d5d615dd4775d71ee778f500bd0c1d3fdf68e lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -20,7 +20,7 @@ GET /api/genomes: returns a list of installed genomes """ - return self.app.genomes.get_dbkeys_with_chrom_info( trans ) + return self.app.genomes.get_dbkeys( trans ) @web.json def show( self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ): diff -r 4a60baf34969dea43d30b4f18094dfd30c167b25 -r f36d5d615dd4775d71ee778f500bd0c1d3fdf68e lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -944,7 +944,7 @@ # Send list of data formats to the upload form so the "extension" select list can be populated dynamically file_formats = trans.app.datatypes_registry.upload_file_formats - dbkeys = trans.app.genomes.get_dbkeys_with_chrom_info( trans ) + dbkeys = trans.app.genomes.get_dbkeys( trans ) # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() if history is not None: diff -r 4a60baf34969dea43d30b4f18094dfd30c167b25 -r f36d5d615dd4775d71ee778f500bd0c1d3fdf68e lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -601,7 +601,7 @@ from the visualization title, but can be edited. This field must contain only lowercase letters, numbers, and the '-' character.""" ) - .add_select( "visualization_dbkey", "Visualization DbKey/Build", value=visualization_dbkey, options=trans.app.genomes.get_dbkeys_with_chrom_info( trans ), error=None) + .add_select( "visualization_dbkey", "Visualization DbKey/Build", value=visualization_dbkey, options=trans.app.genomes.get_dbkeys( trans, chrom_info=True ), error=None) .add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err, help="A description of the visualization; annotation is shown alongside published visualizations."), template="visualization/create.mako" ) @@ -683,7 +683,7 @@ Provide info necessary for creating a new trackster browser. """ return trans.fill_template( "tracks/new_browser.mako", - dbkeys=trans.app.genomes.get_dbkeys_with_chrom_info( trans ), + dbkeys=trans.app.genomes.get_dbkeys( trans, chrom_info=True ), default_dbkey=kwargs.get("default_dbkey", None) ) @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history panel: fix to edit url in failed_metadata hda smallwarningmessage
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4a60baf34969/ changeset: 4a60baf34969 user: carlfeberhard date: 2013-01-25 21:05:38 summary: history panel: fix to edit url in failed_metadata hda smallwarningmessage affected #: 1 file diff -r 982aa4ecc7b5be0d4a4e84b149e47bfc4ef7cc7f -r 4a60baf34969dea43d30b4f18094dfd30c167b25 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -483,7 +483,9 @@ _render_body_failed_metadata : function( parent ){ //TODO: the css for this box is broken (unlike the others) // add a message box about the failure at the top of the body... - parent.append( $( HDABaseView.templates.failedMetadata( this.model.toJSON() ) ) ); + parent.append( $( HDABaseView.templates.failedMetadata( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); //...then render the remaining body as STATES.OK (only diff between these states is the box above) this._render_body_ok( parent ); }, 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: Allow repository owners to reset all repository metadata in the tool shed.
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/982aa4ecc7b5/ changeset: 982aa4ecc7b5 user: greg date: 2013-01-25 19:23:59 summary: Allow repository owners to reset all repository metadata in the tool shed. affected #: 1 file diff -r 3cc16ea80b08e9faa2f721051d89167959aceb2a -r 982aa4ecc7b5be0d4a4e84b149e47bfc4ef7cc7f templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -18,7 +18,7 @@ can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_download = not is_deprecated and not is_new and ( not is_malicious or can_push ) can_rate = not is_new and not is_deprecated and trans.user and repository.user != trans.user - can_reset_all_metadata = not is_deprecated and is_admin and len( repo ) > 0 + can_reset_all_metadata = not is_deprecated and len( repo ) > 0 can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) can_set_metadata = not is_new and not is_deprecated can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip( trans.app ) 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: Handle complex repository dependency definitions in the tool shed.
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3cc16ea80b08/ changeset: 3cc16ea80b08 user: greg date: 2013-01-25 17:48:04 summary: Handle complex repository dependency definitions in the tool shed. affected #: 6 files diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -181,6 +181,7 @@ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=self.app, repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = self.shed_config_dict, relative_install_dir=relative_install_dir, diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1323,9 +1323,8 @@ installed_repository_dependencies, missing_repository_dependencies = get_installed_and_missing_repository_dependencies( trans, repository ) # Handle the current repository's tool dependencies. repository_tool_dependencies = metadata.get( 'tool_dependencies', None ) - repository_installed_tool_dependencies, repository_missing_tool_dependencies = get_installed_and_missing_tool_dependencies( trans, - repository, - repository_tool_dependencies ) + repository_installed_tool_dependencies, repository_missing_tool_dependencies = \ + get_installed_and_missing_tool_dependencies( trans, repository, repository_tool_dependencies ) if reinstalling: installed_tool_dependencies, missing_tool_dependencies = \ populate_tool_dependencies_dicts( trans=trans, diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -103,26 +103,52 @@ defined tool dependencies. The list of tool dependencies may be associated with more than a single repository. """ for dependency_key, requirements_dict in tool_dependencies.items(): - if dependency_key not in [ 'set_environment' ]: - repository_name = requirements_dict.get( 'repository_name', 'unknown' ) - repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) - changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) - dependency_name = requirements_dict[ 'name' ] - version = requirements_dict[ 'version' ] - type = requirements_dict[ 'type' ] - if trans.app.config.tool_dependency_dir: - root_dir = trans.app.config.tool_dependency_dir + if dependency_key in [ 'set_environment' ]: + continue + repository_name = requirements_dict.get( 'repository_name', 'unknown' ) + repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) + changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) + dependency_name = requirements_dict[ 'name' ] + version = requirements_dict[ 'version' ] + type = requirements_dict[ 'type' ] + if trans.app.config.tool_dependency_dir: + root_dir = trans.app.config.tool_dependency_dir + else: + root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>' + install_dir = os.path.join( root_dir, + dependency_name, + version, + repository_owner, + repository_name, + changeset_revision ) + requirements_dict[ 'install_dir' ] = install_dir + tool_dependencies[ dependency_key ] = requirements_dict + return tool_dependencies +def add_tool_shed_orphan_settings_to_tool_dependencies( tool_dependencies, tools ): + """Inspect all received tool dependencies and label those that are orphans within the repository in the tool shed.""" + new_tool_dependencies = {} + if tool_dependencies: + for td_key, requirements_dict in tool_dependencies.items(): + if td_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + type = 'set_environment' + name = set_environment_dict.get( 'name', None ) + version = None + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + set_environment_dict[ 'is_orphan_in_tool_shed' ] = is_orphan_in_tool_shed + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ td_key ] = new_set_environment_dict_list + new_tool_dependencies[ td_key ] = new_set_environment_dict_list else: - root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>' - install_dir = os.path.join( root_dir, - dependency_name, - version, - repository_owner, - repository_name, - changeset_revision ) - requirements_dict[ 'install_dir' ] = install_dir - tool_dependencies[ dependency_key ] = requirements_dict - return tool_dependencies + type = requirements_dict.get( 'type', 'package' ) + name = requirements_dict.get( 'name', None ) + version = requirements_dict.get( 'version', None ) + if type and name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + requirements_dict[ 'is_orphan_in_tool_shed' ] = is_orphan_in_tool_shed + new_tool_dependencies[ td_key ] = requirements_dict + return new_tool_dependencies def add_tool_versions( trans, id, repository_metadata, changeset_revisions ): # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata. metadata = repository_metadata.metadata @@ -316,6 +342,9 @@ if metadata: if 'tool_dependencies' in metadata: tool_dependencies = metadata[ 'tool_dependencies' ] + if trans.webapp.name == 'community': + tools = metadata.get( 'tools', None ) + tool_dependencies = add_tool_shed_orphan_settings_to_tool_dependencies( tool_dependencies, tools ) folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( trans, folder_id, tool_dependencies, @@ -441,55 +470,6 @@ if repository_dependency[ 0:3 ] == partial_rd: return False return True -def can_generate_tool_dependency_metadata( root, metadata_dict ): - """ - Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml - file is defined in the <requirement> tag for at least one tool in the repository. - """ - can_generate_dependency_metadata = False - for elem in root: - tool_dependency_type = elem.tag - tool_dependency_version = elem.get( 'version', None ) - if tool_dependency_type == 'package': - can_generate_dependency_metadata = False - tool_dependency_name = elem.get( 'name', None ) - if tool_dependency_name and tool_dependency_version: - for tool_dict in metadata_dict.get( 'tools', [] ): - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - req_name = requirement_dict.get( 'name', None ) - req_version = requirement_dict.get( 'version', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==tool_dependency_name and req_version==tool_dependency_version and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - if not can_generate_dependency_metadata: - break - elif tool_dependency_type == 'set_environment': - # Here elem is something like: <set_environment version="1.0"> - for env_var_elem in elem: - can_generate_dependency_metadata = False - # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - env_var_name = env_var_elem.get( 'name', None ) - if env_var_name: - for tool_dict in metadata_dict.get( 'tools', [] ): - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - # {"name": "R_SCRIPT_PATH", "type": "set_environment", "version": null} - req_name = requirement_dict.get( 'name', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==env_var_name and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - return can_generate_dependency_metadata def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ): """ Determine if repository's tool config file on disk can be used. This method is restricted to tool config files since, with the @@ -573,7 +553,7 @@ sample_found = True break if not sample_found: - correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file_name ) correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) return invalid_files_and_errors_tups @@ -1007,8 +987,8 @@ for env_elem in elem: env_name = env_elem.get( 'name', None ) if env_name: - requirements_dict [ 'name' ] = env_name - requirements_dict [ 'type' ] = 'set_environment' + requirements_dict[ 'name' ] = env_name + requirements_dict[ 'type' ] = 'set_environment' if requirements_dict: if 'set_environment' in tool_dependencies_dict: tool_dependencies_dict[ 'set_environment' ].append( requirements_dict ) @@ -1051,8 +1031,9 @@ correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end ) message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) return message -def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False ): +def generate_metadata_for_changeset_revision( app, repository, changeset_revision, repository_clone_url, shed_config_dict=None, relative_install_dir=None, + repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's @@ -1202,37 +1183,48 @@ metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files - if 'tools' in metadata_dict: - # This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( app, - repository, - tool_dependencies_config, - metadata_dict, - original_repository_metadata=original_repository_metadata ) + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) + if tool_dependencies_config: + metadata_dict, error_message = generate_tool_dependency_metadata( app, + repository, + changeset_revision, + repository_clone_url, + tool_dependencies_config, + metadata_dict, + original_repository_metadata=original_repository_metadata ) + if error_message: + invalid_file_tups.append( ( 'tool_dependencies.xml', error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. app.config.tool_data_path = original_tool_data_path app.config.tool_data_table_config_path = original_tool_data_table_config_path return metadata_dict, invalid_file_tups -def generate_package_dependency_metadata( elem, tool_dependencies_dict ): +def generate_package_dependency_metadata( app, elem, tool_dependencies_dict ): """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set.""" + repository_dependency_tup = [] requirements_dict = {} + error_message = '' package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) if package_name and package_version: - dependency_key = '%s/%s' % ( package_name, package_version ) - requirements_dict [ 'name' ] = package_name - requirements_dict [ 'version' ] = package_version - requirements_dict [ 'type' ] = 'package' + requirements_dict[ 'name' ] = package_name + requirements_dict[ 'version' ] = package_version + requirements_dict[ 'type' ] = 'package' for sub_elem in elem: if sub_elem.tag == 'readme': requirements_dict[ 'readme' ] = sub_elem.text + elif sub_elem.tag == 'repository': + # We have a complex repository dependency. + current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app=app, + repository_elem=sub_elem, + repository_dependencies_tups=None ) + repository_dependency_tup = current_rd_tups[ 0 ] if requirements_dict: + dependency_key = '%s/%s' % ( package_name, package_version ) tool_dependencies_dict[ dependency_key ] = requirements_dict - return tool_dependencies_dict + return tool_dependencies_dict, repository_dependency_tup, error_message def generate_repository_dependency_metadata_for_installed_repository( app, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method @@ -1281,63 +1273,27 @@ log.debug( error_message ) is_valid = False if is_valid: - sa_session = app.model.context.current for repository_elem in root.findall( 'repository' ): - toolshed = repository_elem.attrib[ 'toolshed' ] - name = repository_elem.attrib[ 'name' ] - owner = repository_elem.attrib[ 'owner'] - changeset_revision = repository_elem.attrib[ 'changeset_revision' ] - user = None - repository = None - if tool_shed_is_this_tool_shed( toolshed ): - try: - user = sa_session.query( app.model.User ) \ - .filter( app.model.User.table.c.username == owner ) \ - .one() - except Exception, e: - error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) - log.debug( error_message ) - return metadata_dict, error_message - if user: - try: - repository = sa_session.query( app.model.Repository ) \ - .filter( and_( app.model.Repository.table.c.name == name, - app.model.Repository.table.c.user_id == user.id ) ) \ - .first() - except: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return metadata_dict, error_message - if repository: - repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) - if repository_dependencies_tup not in repository_dependencies_tups: - repository_dependencies_tups.append( repository_dependencies_tup ) - else: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return metadata_dict, error_message - else: - error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name ) - log.debug( error_message ) - return metadata_dict, error_message - else: - # Repository dependencies are currentlhy supported within a single tool shed. - error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) - error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." + current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups ) + if error_message: log.debug( error_message ) return metadata_dict, error_message + for crdt in current_rd_tups: + repository_dependencies_tups.append( crdt ) if repository_dependencies_tups: repository_dependencies_dict = dict( description=root.get( 'description' ), repository_dependencies=repository_dependencies_tups ) metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict return metadata_dict, error_message -def generate_tool_dependency_metadata( app, repository, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): +def generate_tool_dependency_metadata( app, repository, changeset_revision, repository_clone_url, tool_dependencies_config, metadata_dict, + original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ + error_message = '' if original_repository_metadata: - # Keep a copy of the original tool dependencies dictionary in the metadata. + # Keep a copy of the original tool dependencies dictionary and the list of tool dictionaries in the metadata. original_tool_dependencies_dict = original_repository_metadata.get( 'tool_dependencies', None ) else: original_tool_dependencies_dict = None @@ -1349,24 +1305,49 @@ root = tree.getroot() ElementInclude.include( root ) tool_dependencies_dict = {} - if can_generate_tool_dependency_metadata( root, metadata_dict ): - for elem in root: - if elem.tag == 'package': - tool_dependencies_dict = generate_package_dependency_metadata( elem, tool_dependencies_dict ) - elif elem.tag == 'set_environment': - tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) - # Handle tool dependency installation via other means here (future). - if tool_dependencies_dict: - metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - else: - log.debug( "Name, version and type from the <requirement> tag does not match the information in the tool_dependencies.xml file. Tool dependencies will be ignored." ) + repository_dependency_tups = [] + for elem in root: + if elem.tag == 'package': + tool_dependencies_dict, repository_dependency_tup, message = generate_package_dependency_metadata( app, elem, tool_dependencies_dict ) + if repository_dependency_tup and repository_dependency_tup not in repository_dependency_tups: + repository_dependency_tups.append( repository_dependency_tup ) + if message: + log.debug( message ) + error_message = '%s %s' % ( error_message, message ) + elif elem.tag == 'set_environment': + tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) if tool_dependencies_dict: if original_tool_dependencies_dict: # We're generating metadata on an update pulled to a tool shed repository installed into a Galaxy instance, so handle changes to # tool dependencies appropriately. handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_tool_dependencies_dict, tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - return metadata_dict + if repository_dependency_tups: + tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) + if app.name == 'community': + repository_owner = repository.user.username + else: + repository_owner = repository.owner + rd_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=tool_shed, + repository_name=repository.name, + repository_owner=repository_owner, + changeset_revision=changeset_revision ) + repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', None ) + if repository_dependencies_dict: + if rd_key in repository_dependencies_dict: + repository_dependencies = repository_dependencies_dict[ rd_key ] + for repository_dependency_tup in repository_dependency_tups: + if repository_dependency_tup not in repository_dependencies: + repository_dependencies.append( repository_dependency_tup ) + repository_dependencies_dict[ rd_key ] = repository_dependencies + else: + repository_dependencies_dict[ rd_key ] = repository_dependency_tups + else: + repository_dependencies_dict = dict( root_key=rd_key, + description=root.get( 'description' ), + repository_dependencies=repository_dependency_tups ) + metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict + return metadata_dict, error_message def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): if tool_section is not None: tool_elem = SubElement( tool_section, 'tool' ) @@ -2481,6 +2462,79 @@ message = str( e ) error = True return error, message +def has_orphan_tool_dependencies_in_tool_shed( metadata ): + """Inspect tool dependencies included in the received metadata and determine if any of them are orphans within the repository in the tool shed.""" + if metadata: + tools = metadata.get( 'tools', None ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + for td_key, requirements_dict in tool_dependencies.items(): + if td_key in [ 'set_environment' ]: + for set_environment_dict in requirements_dict: + type = 'set_environment' + name = set_environment_dict.get( 'name', None ) + version = None + if name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + if is_orphan_in_tool_shed: + return True + else: + type = requirements_dict.get( 'type', None ) + name = requirements_dict.get( 'name', None ) + version = requirements_dict.get( 'version', None ) + if type and name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + if is_orphan_in_tool_shed: + return True + return False +def handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups ): + if repository_dependencies_tups is None: + new_rd_tups = [] + else: + new_rd_tups = [ rdt for rdt in repository_dependencies_tups ] + error_message = '' + sa_session = app.model.context.current + toolshed = repository_elem.attrib[ 'toolshed' ] + name = repository_elem.attrib[ 'name' ] + owner = repository_elem.attrib[ 'owner' ] + changeset_revision = repository_elem.attrib[ 'changeset_revision' ] + user = None + repository = None + if tool_shed_is_this_tool_shed( toolshed ): + try: + user = sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == owner ) \ + .one() + except Exception, e: + error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) + log.debug( error_message ) + return new_rd_tups, error_message + if user: + try: + repository = sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() + except: + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) + log.debug( error_message ) + return new_rd_tups, error_message + if repository: + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in new_rd_tups: + new_rd_tups.append( repository_dependencies_tup ) + else: + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) + log.debug( error_message ) + else: + error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name ) + log.debug( error_message ) + else: + # Repository dependencies are currentlhy supported within a single tool shed. + error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) + error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." + log.debug( error_message ) + return new_rd_tups, error_message def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) @@ -2932,6 +2986,7 @@ original_metadata_dict = repository.metadata metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, @@ -3012,6 +3067,7 @@ log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) current_metadata_dict, invalid_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=current_changeset_revision, repository_clone_url=repository_clone_url, relative_install_dir=repo_dir, repository_files_dir=work_dir, @@ -3148,6 +3204,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.tip( trans.app ), repository_clone_url=repository_clone_url, relative_install_dir=repo_dir, repository_files_dir=None, @@ -3197,7 +3254,7 @@ reset_tool_data_tables( trans.app ) return message, status def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ): - # Set metadata on the repository tip. + """Set metadata on the repository tip in the tool shed - this method is not called from Galaxy.""" error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) if error_message: # If there is an error, display it. @@ -3214,6 +3271,32 @@ except: file_name = fpath return file_name +def tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ): + """ + Determine if the combination of the received type, name and version is defined in the <requirement> tag for at least one tool in the received list of tools. + If not, the tool dependency defined by the combination is considered an orphan in it's repository in the tool shed. + """ + if tools: + if type == 'package': + if name and version: + for tool_dict in tools: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_version = requirement_dict.get( 'version', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name == name and req_version == version and req_type == type: + return False + elif type == 'set_environment': + if name: + for tool_dict in tools: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name == name and req_type == type: + return False + return True def to_safe_string( text, to_html=True ): """Translates the characters in text to an html string""" if text: diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -175,11 +175,10 @@ metadata_dict = repository.metadata_revisions[0].metadata else: metadata_dict = {} - if 'tool_dependencies' not in metadata_dict: + if suc.has_orphan_tool_dependencies_in_tool_shed( metadata_dict ): message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", ' - message += 'so the tool dependency definitions will be ignored.' + message += 'so one or more of the defined tool dependencies are considered orphans within this repository.' status = 'warning' - log.debug( 'Error in tool dependencies for repository with id %s and name %s: %s' % ( str( repository.id ), str( repository.name ), message ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. suc.reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository', diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a 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 @@ -102,7 +102,7 @@ class ToolDependency( object ): """Tool dependency object""" def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None, - tool_dependency_id=None ): + tool_dependency_id=None, is_orphan=None ): self.id = id self.name = name self.version = version @@ -112,6 +112,7 @@ self.installation_status = installation_status self.repository_id = repository_id self.tool_dependency_id = tool_dependency_id + self.is_orphan = is_orphan @property def listify( self ): return [ self.name, self.version, self.type ] @@ -322,17 +323,35 @@ version='Version', type='Type', install_dir='Install directory', - installation_status='Installation status' ) + readme=None, + installation_status='Installation status', + repository_id=None, + tool_dependency_id=None, + is_orphan=None ) else: tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', version='Version', - type='Type' ) + type='Type', + install_dir=None, + readme=None, + installation_status=None, + repository_id=None, + tool_dependency_id=None, + is_orphan=None ) folder.tool_dependencies.append( tool_dependency ) + is_orphan_description = "these dependencies may not be required by tools in this repository" for dependency_key, requirements_dict in tool_dependencies.items(): tool_dependency_id += 1 - if dependency_key == 'set_environment': + if dependency_key in [ 'set_environment' ]: for set_environment_dict in requirements_dict: + if trans.webapp.name == 'community': + is_orphan = set_environment_dict.get( 'is_orphan_in_tool_shed', False ) + else: + # TODO: handle this is Galaxy + is_orphan = False + if is_orphan: + folder.description = is_orphan_description name = set_environment_dict.get( 'name', None ) type = set_environment_dict[ 'type' ] repository_id = set_environment_dict.get( 'repository_id', None ) @@ -343,12 +362,23 @@ installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, name=name, + version=None, type=type, + install_dir=None, + readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id ) + tool_dependency_id=td_id, + is_orphan=is_orphan ) folder.tool_dependencies.append( tool_dependency ) else: + if trans.webapp.name == 'community': + is_orphan = requirements_dict.get( 'is_orphan_in_tool_shed', False ) + else: + # TODO: handle this is Galaxy + is_orphan = False + if is_orphan: + folder.description = is_orphan_description name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] @@ -364,9 +394,11 @@ version=version, type=type, install_dir=install_dir, + readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id ) + tool_dependency_id=td_id, + is_orphan=is_orphan ) folder.tool_dependencies.append( tool_dependency ) else: tool_dependencies_root_folder = None diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a 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 @@ -661,6 +661,7 @@ shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict=shed_config_dict, relative_install_dir=relative_install_dir, @@ -1692,6 +1693,7 @@ original_metadata_dict = repository.metadata metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, @@ -1887,6 +1889,7 @@ # Update the repository metadata. metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=latest_changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Cuffcompare wrapper fixes + update test files for v2.0.2
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b99d93d0f137/ changeset: b99d93d0f137 user: jgoecks date: 2013-01-25 00:02:22 summary: Cuffcompare wrapper fixes + update test files for v2.0.2 affected #: 2 files diff -r 5fda62776e3d09702d18ba7a1e4a106425949f15 -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ b/test-data/cuffcompare_out7.txt @@ -1,5 +1,5 @@ -# Cuffcompare v1.3.0 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/010/dataset_10703.dat -R ./input1 ./input2 +# Cuffcompare v2.0.2 | Command line was: +#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 # #= Summary for dataset: ./input1 : diff -r 5fda62776e3d09702d18ba7a1e4a106425949f15 -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -78,7 +78,7 @@ <outputs><data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" from_work_dir="cc_output.stats" /> - <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: ${first_input.hid} data tmap file" + <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${first_input.hid} tmap file" from_work_dir="cc_output.input1.tmap" /><data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${first_input.hid} refmap file" @@ -86,12 +86,12 @@ <filter>annotation['use_ref_annotation'] == 'Yes'</filter></data><data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} tmap file" from_work_dir="cc_output.input2.tmap"> - <filter>len( input_files ) > 1</filter> + <filter>len( input_files ) >= 1</filter></data><data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} refmap file" from_work_dir="cc_output.input2.refmap"> - <filter>annotation['use_ref_annotation'] == 'Yes' and len( input_files ) > 1</filter> + <filter>annotation['use_ref_annotation'] == 'Yes' and len( input_files ) >= 1</filter></data><data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"><filter>len( input_files ) > 0</filter> 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: Enable BedGraph to be used as input to wig-to-bigwig tool.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5fda62776e3d/ changeset: 5fda62776e3d user: jgoecks date: 2013-01-24 23:06:51 summary: Enable BedGraph to be used as input to wig-to-bigwig tool. affected #: 3 files diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 test-data/1.bedgraph --- /dev/null +++ b/test-data/1.bedgraph @@ -0,0 +1,30 @@ +chr1 0 14361 0 +chr1 14361 14829 1 +chr1 14829 14969 0 +chr1 14969 15038 1 +chr1 15038 15795 0 +chr1 15795 15947 1 +chr1 15947 16606 0 +chr1 16606 16765 1 +chr1 16765 16857 0 +chr1 16857 17055 1 +chr1 17055 17232 0 +chr1 17232 17368 1 +chr1 17368 17605 0 +chr1 17605 17742 1 +chr1 17742 17914 0 +chr1 17914 18061 1 +chr1 18061 18267 0 +chr1 18267 18366 1 +chr1 18366 24737 0 +chr1 24737 24891 1 +chr1 24891 29320 0 +chr1 29320 29370 1 +chr1 29370 34610 0 +chr1 34610 35174 2 +chr1 35174 35276 0 +chr1 35276 35481 2 +chr1 35481 35720 0 +chr1 35720 36081 2 +chr1 36081 69090 0 +chr1 69090 69093 3 diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 test-data/3.bigwig Binary file test-data/3.bigwig has changed diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 tools/filters/wig_to_bigwig.xml --- a/tools/filters/wig_to_bigwig.xml +++ b/tools/filters/wig_to_bigwig.xml @@ -1,4 +1,4 @@ -<tool id="wig_to_bigWig" name="Wig-to-bigWig" version="1.1.0"> +<tool id="wig_to_bigWig" name="Wig/BedGraph-to-bigWig" version="1.1.0"><description>converter</description><command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 #if $settings.settingsType == "full": @@ -11,7 +11,7 @@ <requirement type="package">ucsc_tools</requirement></requirements><inputs> - <param format="wig" name="input1" type="data" label="Convert"> + <param format="wig,bedgraph" name="input1" type="data" label="Convert"><validator type="unspecified_build" /></param><conditional name="settings"> @@ -46,11 +46,16 @@ <param name="settingsType" value="preset" /><output name="out_file1" file="2.bigwig"/></test> + <test> + <param name="input1" value="1.bedgraph" dbkey="hg19" ftype="bedgraph"/> + <param name="settingsType" value="preset" /> + <output name="out_file1" file="3.bigwig"/> + </test></tests><help> **Syntax** -This tool converts wiggle data into bigWig type. +This tool converts bedgraph or wiggle data into bigWig type. - **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. @@ -71,5 +76,9 @@ dataValue1 dataValue2 +- The **BedGraph format** is described in detail at the `UCSC Bioinformatics website`_ + +.. _UCSC Bioinformatics website: http://genome.ucsc.edu/goldenPath/help/bedgraph.html + </help></tool> 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: inithello: Update test data for kCCA to allow for a wider range of possible output values.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3c243143d68b/ changeset: 3c243143d68b user: inithello date: 2013-01-24 17:09:43 summary: Update test data for kCCA to allow for a wider range of possible output values. affected #: 1 file diff -r c901bbb4eca8142b442fa348b8136d4ff3bcfaf8 -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e test-data/kcca_out1.tabular --- a/test-data/kcca_out1.tabular +++ b/test-data/kcca_out1.tabular @@ -256,7 +256,7 @@ 1\d*\ \-?0\.001\d*\ \-?0\.001\d*\ \-?0\.013\d*\ \-?0\.013\d* 1\d*\ \-?0\.0017\d*\ \-?0\.0017\d*\ \-?0\.011\d*\ \-?0\.011\d* 1\d*\ \-?0\.0024\d*\ \-?0\.0024\d*\ \-?0\.008\d*\ \-?0\.008\d* -1\d*\ \-?8\.7\d*e\-?\d*\ \-?8\.7\d*e\-?\d*\ \-?0\.00049\d*\ \-?0\.00049\d* +1\d*\ \-?8\.[6-8]\d*e\-?\d*\ \-?8\.[6-8]\d*e\-?\d*\ \-?0\.00049\d*\ \-?0\.00049\d* 1\d*\ \-?0\.0007\d*\ \-?0\.0007\d*\ \-?7\.8\d*e\-?\d*\ \-?7\.8\d*e\-?\d* 1\d*\ \-?0\.00075\d*\ \-?0\.00075\d*\ \-?0\.056\d*\ \-?0\.056\d* 1\d*\ \-?0\.004\d*\ \-?0\.004\d*\ \-?0\.04\d*\ \-?0\.04\d* @@ -291,7 +291,7 @@ 1\d*\ \-?0\.0053\d*\ \-?0\.0053\d*\ \-?0\.0019\d*\ \-?0\.0019\d* 1\d*\ \-?0\.0021\d*\ \-?0\.0021\d*\ \-?0\.0096\d*\ \-?0\.0096\d* 1\d*\ \-?0\.0010\d*\ \-?0\.0010\d*\ \-?0\.038\d*\ \-?0\.038\d* -1\d*\ \-?3\.5\d*e-\d*\ \-?3\.5\d*e-\d*\ \-?0\.0081\d*\ \-?0\.0081\d* +1\d*\ \-?3\.[4-6]\d*e-\d*\ \-?3\.[4-6]\d*e-\d*\ \-?0\.0081\d*\ \-?0\.0081\d* 1\d*\ \-?0\.0053\d*\ \-?0\.0053\d*\ \-?0\.0019\d*\ \-?0\.0019\d* 1\d*\ \-?0\.0038\d*\ \-?0\.0038\d*\ \-?0\.0085\d*\ \-?0\.0085\d* 1\d*\ \-?0\.001\d*\ \-?0\.001\d*\ \-?0\.013\d*\ \-?0\.013\d* 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: Tasks: Adjust the id_tag to use the format "<jobid>_<taskid>", instead of "<jobid>:<taskid>". This resolves issues with particular cluster runners being able to submit.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c901bbb4eca8/ changeset: c901bbb4eca8 user: dannon date: 2013-01-24 17:03:49 summary: Tasks: Adjust the id_tag to use the format "<jobid>_<taskid>", instead of "<jobid>:<taskid>". This resolves issues with particular cluster runners being able to submit. affected #: 1 file diff -r 6189b2690b4688c4e35066bf09aaf95e1c272d5e -r c901bbb4eca8142b442fa348b8136d4ff3bcfaf8 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -346,7 +346,7 @@ Return an id tag suitable for identifying the task. This combines the task's job id and the task's own id. """ - return "%s:%s" % ( self.job.get_id(), self.get_id() ) + return "%s_%s" % ( self.job.get_id(), self.get_id() ) def get_command_line( self ): return self.command_line def get_parameters( 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: inithello: Functional test to verify correct display of tool migration stages.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6189b2690b46/ changeset: 6189b2690b46 user: inithello date: 2013-01-24 15:29:29 summary: Functional test to verify correct display of tool migration stages. affected #: 2 files diff -r aa8298344ed5b5f7c209a4341999815d25a2e305 -r 6189b2690b4688c4e35066bf09aaf95e1c272d5e test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -667,6 +667,10 @@ ( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def load_galaxy_tool_migrations_page( self, strings_displayed=[], strings_not_displayed=[] ): + url = '/admin/review_tool_migration_stages' + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def load_workflow_image_in_tool_shed( self, repository, workflow_name, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): if not changeset_revision: changeset_revision = self.get_repository_tip( repository ) diff -r aa8298344ed5b5f7c209a4341999815d25a2e305 -r 6189b2690b4688c4e35066bf09aaf95e1c272d5e test/tool_shed/functional/test_1400_review_migration_stages.py --- /dev/null +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -0,0 +1,30 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +class TestToolMigrationStages( ShedTwillTestCase ): + '''Verify that the migration stages display correctly.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_load_migration_stages_page( self ): + '''Load the migration page and check for the appropriate migration stages.''' + stages = [ + 'emboss_5', 'emboss_datatypes', 'emboss', '5.0.0', '0002_tools.sh', + 'freebayes', '0.9.4_a46483351fd0196637614121868fb5c386612b55', 'samtools', '0.1.18', 'FreeBayes requires g++', + 'ncurses', 'zlib', '0003_tools.sh', + 'ncbi_blast_plus', 'blast_datatypes', 'blast+', '2.2.26+', 'blast.ncbi.nlm.nih.gov', 'NCBI BLAST+ tools', '0004_tools.sh', + 'bwa_wrappers', '0.5.9', 'zlib and libpthread', 'Map with BWA for Illumina', '0005_tools.sh', + 'picard', '1.56.0', 'FASTQ to BAM', '0006_tools.sh', + 'lastz', '1.02.00', 'bowtie', '0.12.7', 'Map with Bowtie for Illumina', 'Bowtie requires libpthread', '0007_tools.sh' + ] + self.load_galaxy_tool_migrations_page( strings_displayed=stages ) + 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: inithello: Make wrapper compatible with python 2.5.
by Bitbucket 23 Jan '13

23 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aa8298344ed5/ changeset: aa8298344ed5 user: inithello date: 2013-01-23 18:32:05 summary: Make wrapper compatible with python 2.5. affected #: 1 file diff -r da970ef6075702286d47b9ccf83942092eaac27d -r aa8298344ed5b5f7c209a4341999815d25a2e305 tools/evolution/add_scores.py --- a/tools/evolution/add_scores.py +++ b/tools/evolution/add_scores.py @@ -17,11 +17,11 @@ def open_or_die( filename, mode='r', message=None ): if message is None: - message = 'Error opening {0}'.format( filename ) + message = 'Error opening %s' % filename try: fh = open( filename, mode ) except IOError, err: - die( '{0}: {1}'.format( message, err.strerror ) ) + die( '%s: %s' % ( message, err.strerror ) ) return fh ################################################################################ @@ -48,16 +48,16 @@ if not line.startswith( self.comment_chars ): elems = line.split( self.delimiter ) if len( elems ) <= self.key_column: - die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) ) + die( 'Location file %s line %d: less than %d columns' % ( self.filename, line_number, self.key_column + 1 ) ) else: key = elems.pop( self.key_column ) if key in self._map: if self._map[key] != elems: - die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) ) + die( 'Location file %s line %d: duplicate key "%s"' % ( self.filename, line_number, key ) ) else: self._map[key] = elems except IOError, err: - die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) ) + die( 'Error opening location file %s: %s' % ( self.filename, err.strerror ) ) def get_values( self, key ): if key in self._map: @@ -67,7 +67,7 @@ else: return rval else: - die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) ) + die( 'key "%s" not found in location file %s' % ( key, self.filename ) ) ################################################################################ @@ -77,10 +77,10 @@ # open input, output, and bigwig files location_file = LocationFile( loc_filename ) bigwig_filename = location_file.get_values( loc_key ) - bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file {0}'.format( bigwig_filename ) ) + bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file %s' % bigwig_filename ) bw = BigWigFile( file=bwfh ) - ifh = open_or_die( input_filename, message='Error opening input file {0}'.format( input_filename ) ) - ofh = open_or_die( output_filename, mode='w', message='Error opening output file {0}'.format( output_filename ) ) + ifh = open_or_die( input_filename, message='Error opening input file %s' % input_filename ) + ofh = open_or_die( output_filename, mode='w', message='Error opening output file %s' % output_filename ) # make column numbers 0-based chrom_col = int( chrom_col ) - 1 @@ -101,11 +101,11 @@ score_list_len = len( score_list ) if score_list_len == 1: beg, end, score = score_list[0] - score_val = '{0:1.3f}'.format( score ) + score_val = '%1.3f' % score elif score_list_len == 0: score_val = 'NA' else: - die( '{0} line {1}: chrom={2}, start={3}, score_list_len = {4}'.format( input_filename, line_number, chrom, start, score_list_len ) ) + die( '%s line %d: chrom=%s, start=%d, score_list_len = %d' % ( input_filename, line_number, chrom, start, score_list_len ) ) print >> ofh, '\t'.join( [line, score_val] ) else: print >> ofh, line 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: dan: Add missing import in galaxy.util. Fixes bug in .mkstemp_ln().
by Bitbucket 23 Jan '13

23 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da970ef60757/ changeset: da970ef60757 user: dan date: 2013-01-23 18:27:12 summary: Add missing import in galaxy.util. Fixes bug in .mkstemp_ln(). affected #: 1 file diff -r 3c752f2d4d958f34f085f2cc707c503693b4680d -r da970ef6075702286d47b9ccf83942092eaac27d lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -2,7 +2,7 @@ Utility functions used systemwide. """ -import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib +import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib, errno from email.MIMEText import MIMEText # Older py compatibility 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 22 Jan '13

22 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b368163e14fe/ changeset: b368163e14fe user: inithello date: 2013-01-22 21:54:49 summary: Update functional test parameters so tests will pass. affected #: 2 files diff -r 2f3e80ded864f29b27ad3af71f4887f23293297c -r b368163e14fe6b2fd3d5a5f2b8cb90ef7990677b tools/phenotype_association/dividePgSnpAlleles.xml --- a/tools/phenotype_association/dividePgSnpAlleles.xml +++ b/tools/phenotype_association/dividePgSnpAlleles.xml @@ -25,7 +25,7 @@ <tests><test><param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' /> - <param name='refcol' value='no' /> + <param name='ref' value='no' /><output name="output" file="dividePgSnp_output.txt" /></test></tests> diff -r 2f3e80ded864f29b27ad3af71f4887f23293297c -r b368163e14fe6b2fd3d5a5f2b8cb90ef7990677b tools/phenotype_association/snpFreq.xml --- a/tools/phenotype_association/snpFreq.xml +++ b/tools/phenotype_association/snpFreq.xml @@ -44,6 +44,7 @@ <tests><test> + <param name="inType" value="tab" /><param name="input" ftype="tabular" value="snpFreqInput.txt" dbkey="hg18" /><param name="group1_1" value="4" /><param name="group1_2" value="5" /> https://bitbucket.org/galaxy/galaxy-central/commits/3c752f2d4d95/ changeset: 3c752f2d4d95 user: inithello date: 2013-01-22 21:55:29 summary: Make wrapper compatible with python 2.5. affected #: 1 file diff -r b368163e14fe6b2fd3d5a5f2b8cb90ef7990677b -r 3c752f2d4d958f34f085f2cc707c503693b4680d tools/evolution/add_scores.py --- a/tools/evolution/add_scores.py +++ b/tools/evolution/add_scores.py @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import with_statement import sys from galaxy import eggs 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: Handle invalid repository dependency definitions contained in tool shed repositories.
by Bitbucket 22 Jan '13

22 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f3e80ded864/ changeset: 2f3e80ded864 user: greg date: 2013-01-22 19:24:23 summary: Handle invalid repository dependency definitions contained in tool shed repositories. affected #: 2 files diff -r 0e064a23864c846483b35f893cf0a769dedf24f1 -r 2f3e80ded864f29b27ad3af71f4887f23293297c lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1888,6 +1888,7 @@ handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) elif key_rd_dicts_to_be_processed: handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies ) return all_repository_dependencies def get_repository_dependency_as_key( repository_dependency ): return container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], @@ -2181,12 +2182,12 @@ for key_rd_dict in key_rd_dicts: key = key_rd_dict.keys()[ 0 ] repository_dependency = key_rd_dict[ key ] - toolshed, name, owner, changeset_revision = repository_dependency - if tool_shed_is_this_tool_shed( toolshed ): - repository = get_repository_by_name_and_owner( trans, name, owner ) + rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency + if tool_shed_is_this_tool_shed( rd_toolshed ): + repository = get_repository_by_name_and_owner( trans, rd_name, rd_owner ) repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( repository.id ), - changeset_revision ) + rd_changeset_revision ) if repository_metadata: # The repository changeset_revision is installable, so no updates are available. new_key_rd_dict = {} @@ -2196,15 +2197,20 @@ # The repository changeset_revision is no longer installable, so see if there's been an update. repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) - changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + changeset_revision = get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision ) repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: new_key_rd_dict = {} - new_key_rd_dict[ key ] = [ toolshed, name, owner, repository_metadata.changeset_revision ] + new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision ] # We have the updated changset revision. updated_key_rd_dicts.append( new_key_rd_dict ) + else: + toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ + ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) + log.debug( message ) return updated_key_rd_dicts def get_url_from_repository_tool_shed( app, repository ): """ @@ -2816,6 +2822,25 @@ new_key_rd_dict[ current_repository_key ] = repository_dependency key_rd_dicts_to_be_processed.append( new_key_rd_dict ) return filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies +def prune_invalid_repository_dependencies( repository_dependencies ): + """ + Eliminate all invalid entries in the received repository_dependencies dictionary. An entry is invalid if if the value_list of the key/value pair is + empty. This occurs when an invalid combination of tool shed, name , owner, changeset_revision is used and a repository_metadata reocrd is not found. + """ + valid_repository_dependencies = {} + description = repository_dependencies.get( 'description', None ) + root_key = repository_dependencies.get( 'root_key', None ) + if root_key is None: + return valid_repository_dependencies + for key, value in repository_dependencies.items(): + if key in [ 'description', 'root_key' ]: + continue + if value: + valid_repository_dependencies[ key ] = value + if valid_repository_dependencies: + valid_repository_dependencies[ 'description' ] = description + valid_repository_dependencies[ 'root_key' ] = root_key + return valid_repository_dependencies def remove_dir( dir ): if os.path.exists( dir ): try: diff -r 0e064a23864c846483b35f893cf0a769dedf24f1 -r 2f3e80ded864f29b27ad3af71f4887f23293297c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1909,6 +1909,7 @@ metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious if repository_metadata: + metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, repository=repository, @@ -1917,6 +1918,12 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) + if metadata: + if 'repository_dependencies' in metadata and not repository_dependencies: + message += 'The repository dependency definitions for this repository are invalid and will be ignored. Make sure valid <b>toolshed</b>, ' + message += '<b>name</b>, <b>owner</b> and <b>changeset_revision</b> values are defined in the contained <b>repository_dependencies.xml</b> ' + message += 'file to correct this problem.' + status = 'error' if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push @@ -2029,6 +2036,10 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) + if metadata: + if 'repository_dependencies' in metadata and not repository_dependencies: + message += 'The repository dependency definitions for this repository are invalid and will be ignored.' + status = 'error' else: repository_metadata_id = None metadata = None @@ -2550,6 +2561,10 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) + if metadata: + if 'repository_dependencies' in metadata and not repository_dependencies: + message += 'The repository dependency definitions for this repository are invalid and will be ignored.' + status = 'error' else: repository_metadata_id = None metadata = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Exporting workflows: (a) remove spurious header and (b) add option to create workflow image. (b) inspired by Björn Grüning
by Bitbucket 21 Jan '13

21 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0e064a23864c/ changeset: 0e064a23864c user: jgoecks date: 2013-01-21 15:02:56 summary: Exporting workflows: (a) remove spurious header and (b) add option to create workflow image. (b) inspired by Björn Grüning affected #: 1 file diff -r bb3a803c207d4e1f305982bf97bcb9019810bd83 -r 0e064a23864c846483b35f893cf0a769dedf24f1 templates/workflow/export.mako --- a/templates/workflow/export.mako +++ b/templates/workflow/export.mako @@ -25,7 +25,6 @@ <h3>Export to myExperiment</h3><div class="toolForm"> - <div class="toolFormTitle">Export</div><form action="${h.url_for( action='export_to_myexp', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"> @@ -46,6 +45,13 @@ <%def name="render_more(item)"> ## Add form to export to myExperiment. ${self.render_export_to_myexp(item)} + + ## Add link to render as SVG image. + <h3>Create Image</h3> + + <a href="${h.url_for( action='gen_image', id=trans.security.encode_id( item.id ) )}"> + Create image of ${get_class_display_name( item.__class__ ).lower()} in SVG format + </a></%def><%def name="center_panel()"> 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: Eliminate the tool shed's common controller.
by Bitbucket 21 Jan '13

21 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bb3a803c207d/ changeset: bb3a803c207d user: greg date: 2013-01-21 14:59:31 summary: Eliminate the tool shed's common controller. affected #: 4 files diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ /dev/null @@ -1,27 +0,0 @@ -import logging -from galaxy.model.item_attrs import UsesItemRatings - -log = logging.getLogger( __name__ ) - -class ItemRatings( UsesItemRatings ): - """Overrides rate_item method since we also allow for comments""" - def rate_item( self, trans, user, item, rating, comment='' ): - """ Rate an item. Return type is <item_class>RatingAssociation. """ - item_rating = self.get_user_item_rating( trans.sa_session, user, item, webapp_model=trans.model ) - if not item_rating: - # User has not yet rated item; create rating. - item_rating_assoc_class = self._get_item_rating_assoc_class( item, webapp_model=trans.model ) - item_rating = item_rating_assoc_class() - item_rating.user = trans.user - item_rating.set_item( item ) - item_rating.rating = rating - item_rating.comment = comment - trans.sa_session.add( item_rating ) - trans.sa_session.flush() - elif item_rating.rating != rating or item_rating.comment != comment: - # User has previously rated item; update rating. - item_rating.rating = rating - item_rating.comment = comment - trans.sa_session.add( item_rating ) - trans.sa_session.flush() - return item_rating diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -13,7 +13,7 @@ import galaxy.util.shed_util_common as suc from galaxy.tool_shed import encoding_util from galaxy.webapps.community.util import workflow_util -import common +from galaxy.webapps.community.util import common_util import galaxy.tools from galaxy import eggs @@ -518,7 +518,7 @@ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ) -class RepositoryController( BaseUIController, common.ItemRatings ): +class RepositoryController( BaseUIController, common_util.ItemRatings ): install_matched_repository_grid = InstallMatchedRepositoryGrid() matched_repository_grid = MatchedRepositoryGrid() diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -6,7 +6,7 @@ from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_ from sqlalchemy.sql.expression import func -import common +from galaxy.webapps.community.util import common_util from galaxy.webapps.community.util.container_util import STRSEP from repository import RepositoryGrid import galaxy.util.shed_util_common as suc @@ -260,7 +260,7 @@ .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) -class RepositoryReviewController( BaseUIController, common.ItemRatings ): +class RepositoryReviewController( BaseUIController, common_util.ItemRatings ): component_grid = ComponentGrid() repositories_reviewed_by_me_grid = RepositoriesReviewedByMeGrid() diff -r 34404f8489792a97096b36f012fbf775cc3b382b -r bb3a803c207d4e1f305982bf97bcb9019810bd83 lib/galaxy/webapps/community/util/common_util.py --- /dev/null +++ b/lib/galaxy/webapps/community/util/common_util.py @@ -0,0 +1,27 @@ +import logging +from galaxy.model.item_attrs import UsesItemRatings + +log = logging.getLogger( __name__ ) + +class ItemRatings( UsesItemRatings ): + """Overrides rate_item method since we also allow for comments""" + def rate_item( self, trans, user, item, rating, comment='' ): + """ Rate an item. Return type is <item_class>RatingAssociation. """ + item_rating = self.get_user_item_rating( trans.sa_session, user, item, webapp_model=trans.model ) + if not item_rating: + # User has not yet rated item; create rating. + item_rating_assoc_class = self._get_item_rating_assoc_class( item, webapp_model=trans.model ) + item_rating = item_rating_assoc_class() + item_rating.user = trans.user + item_rating.set_item( item ) + item_rating.rating = rating + item_rating.comment = comment + trans.sa_session.add( item_rating ) + trans.sa_session.flush() + elif item_rating.rating != rating or item_rating.comment != comment: + # User has previously rated item; update rating. + item_rating.rating = rating + item_rating.comment = comment + trans.sa_session.add( item_rating ) + trans.sa_session.flush() + return item_rating Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add missing import to update manager.
by Bitbucket 19 Jan '13

19 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/34404f848979/ changeset: 34404f848979 user: greg date: 2013-01-19 23:54:48 summary: Add missing import to update manager. affected #: 1 file diff -r 7d37ffe813f2a037b560af26770ffe5924ae643f -r 34404f8489792a97096b36f012fbf775cc3b382b lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -4,6 +4,7 @@ import threading, urllib2, logging from galaxy.util import string_as_bool import galaxy.util.shed_util as shed_util +from galaxy.model.orm import and_ 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 19 Jan '13

19 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0df1612c1cb1/ changeset: 0df1612c1cb1 user: asbardellati date: 2013-01-18 17:11:04 summary: Add option for writing not aligned reads to file Reviewed-by: Nicola Soranzo <soranzo(a)crs4.it> affected #: 2 files diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r 0df1612c1cb14b48f5bee405a04886de5380df39 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -31,10 +31,29 @@ parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' ) parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' ) + parser.add_option( '', '--output_unaligned_reads', dest='output_unaligned_reads', help='File name for unaligned reads (single-end)' ) + parser.add_option( '', '--output_unaligned_reads_l', dest='output_unaligned_reads_l', help='File name for unaligned reads (left, paired-end)' ) + parser.add_option( '', '--output_unaligned_reads_r', dest='output_unaligned_reads_r', help='File name for unaligned reads (right, paired-end)' ) + (options, args) = parser.parse_args() + tmp_unaligned_file_name = None # Creat bowtie index if necessary. tmp_index_dir = tempfile.mkdtemp() + + if options.single_paired == 'paired': + if options.output_unaligned_reads_l and options.output_unaligned_reads_r: + tmp_unaligned_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' ) + tmp_unaligned_file_name = tmp_unaligned_file.name + tmp_unaligned_file.close() + output_unaligned_reads = '--un-conc %s' % tmp_unaligned_file_name + else: + output_unaligned_reads = '' + elif options.output_unaligned_reads: + output_unaligned_reads = '--un %s' % options.output_unaligned_reads + else: + output_unaligned_reads = '' + if options.own_file: index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) ) try: @@ -71,7 +90,7 @@ index_path = options.index_path # Build bowtie command; use view and sort to create sorted bam. - cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s' + cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s' # Set up reads. if options.single_paired == 'paired': @@ -104,7 +123,7 @@ opts += ' --rg %s:%s' % ( 'SM', options.rgsm ) # Final command: - cmd = cmd % ( opts, index_path, reads, options.output ) + cmd = cmd % ( opts, index_path, reads, output_unaligned_reads, options.output ) print cmd # Run @@ -136,6 +155,16 @@ except Exception, e: stop_err( 'Error in bowtie2:\n' + str( e ) ) + # get unaligned reads output files in place if appropriate + if options.single_paired == 'paired' and tmp_unaligned_file_name and options.output_unaligned_reads_l and options.output_unaligned_reads_r: + try: + left = tmp_unaligned_file_name.replace( '.fastq', '.1.fastq' ) + right = tmp_unaligned_file_name.replace( '.fastq', '.2.fastq' ) + shutil.move( left, options.output_unaligned_reads_l ) + shutil.move( right, options.output_unaligned_reads_r ) + except Exception, e: + sys.stdout.write( 'Error producing the unaligned output files.\n' ) + # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r 0df1612c1cb14b48f5bee405a04886de5380df39 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -1,6 +1,6 @@ <tool id="bowtie2" name="Bowtie2" version="0.1"> - <description>is a short-read mapper</description> + <description>is a short-read aligner</description><version_command>bowtie2 --version</version_command><requirements><requirement type="package">bowtie2</requirement> @@ -15,6 +15,17 @@ ## Outputs. --output=$output + #if str( $singlePaired.sPaired ) == "single" + #if $output_unaligned_reads_l + --output_unaligned_reads=$output_unaligned_reads_l + #end if + #else + #if $output_unaligned_reads_l and $output_unaligned_reads_r + --output_unaligned_reads_l=$output_unaligned_reads_l + --output_unaligned_reads_r=$output_unaligned_reads_r + #end if + #end if + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile @@ -71,6 +82,7 @@ <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional> + <param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and --un-conc for paired-ends)" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option> @@ -133,7 +145,7 @@ </inputs><outputs> - <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> @@ -152,6 +164,22 @@ </conditional></actions></data> + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > + <filter>unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> + <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data></outputs><tests> https://bitbucket.org/galaxy/galaxy-central/commits/7d37ffe813f2/ changeset: 7d37ffe813f2 user: jgoecks date: 2013-01-19 22:35:28 summary: Merged in nsoranzo/galaxy-central (pull request #110) Add option to bowtie2 tool for writing not aligned reads to file affected #: 2 files diff -r 50c65739cd1af36f48672a980db378783dffcdd5 -r 7d37ffe813f2a037b560af26770ffe5924ae643f tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -31,10 +31,29 @@ parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' ) parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' ) + parser.add_option( '', '--output_unaligned_reads', dest='output_unaligned_reads', help='File name for unaligned reads (single-end)' ) + parser.add_option( '', '--output_unaligned_reads_l', dest='output_unaligned_reads_l', help='File name for unaligned reads (left, paired-end)' ) + parser.add_option( '', '--output_unaligned_reads_r', dest='output_unaligned_reads_r', help='File name for unaligned reads (right, paired-end)' ) + (options, args) = parser.parse_args() + tmp_unaligned_file_name = None # Creat bowtie index if necessary. tmp_index_dir = tempfile.mkdtemp() + + if options.single_paired == 'paired': + if options.output_unaligned_reads_l and options.output_unaligned_reads_r: + tmp_unaligned_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' ) + tmp_unaligned_file_name = tmp_unaligned_file.name + tmp_unaligned_file.close() + output_unaligned_reads = '--un-conc %s' % tmp_unaligned_file_name + else: + output_unaligned_reads = '' + elif options.output_unaligned_reads: + output_unaligned_reads = '--un %s' % options.output_unaligned_reads + else: + output_unaligned_reads = '' + if options.own_file: index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) ) try: @@ -71,7 +90,7 @@ index_path = options.index_path # Build bowtie command; use view and sort to create sorted bam. - cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s' + cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s' # Set up reads. if options.single_paired == 'paired': @@ -104,7 +123,7 @@ opts += ' --rg %s:%s' % ( 'SM', options.rgsm ) # Final command: - cmd = cmd % ( opts, index_path, reads, options.output ) + cmd = cmd % ( opts, index_path, reads, output_unaligned_reads, options.output ) print cmd # Run @@ -136,6 +155,16 @@ except Exception, e: stop_err( 'Error in bowtie2:\n' + str( e ) ) + # get unaligned reads output files in place if appropriate + if options.single_paired == 'paired' and tmp_unaligned_file_name and options.output_unaligned_reads_l and options.output_unaligned_reads_r: + try: + left = tmp_unaligned_file_name.replace( '.fastq', '.1.fastq' ) + right = tmp_unaligned_file_name.replace( '.fastq', '.2.fastq' ) + shutil.move( left, options.output_unaligned_reads_l ) + shutil.move( right, options.output_unaligned_reads_r ) + except Exception, e: + sys.stdout.write( 'Error producing the unaligned output files.\n' ) + # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) diff -r 50c65739cd1af36f48672a980db378783dffcdd5 -r 7d37ffe813f2a037b560af26770ffe5924ae643f tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -1,6 +1,6 @@ <tool id="bowtie2" name="Bowtie2" version="0.1"> - <description>is a short-read mapper</description> + <description>is a short-read aligner</description><version_command>bowtie2 --version</version_command><requirements><requirement type="package">bowtie2</requirement> @@ -15,6 +15,17 @@ ## Outputs. --output=$output + #if str( $singlePaired.sPaired ) == "single" + #if $output_unaligned_reads_l + --output_unaligned_reads=$output_unaligned_reads_l + #end if + #else + #if $output_unaligned_reads_l and $output_unaligned_reads_r + --output_unaligned_reads_l=$output_unaligned_reads_l + --output_unaligned_reads_r=$output_unaligned_reads_r + #end if + #end if + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile @@ -71,6 +82,7 @@ <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional> + <param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and --un-conc for paired-ends)" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option> @@ -133,7 +145,7 @@ </inputs><outputs> - <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> @@ -152,6 +164,22 @@ </conditional></actions></data> + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > + <filter>unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> + <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter> + <actions> + <action type="format"> + <option type="from_param" name="singlePaired.input1" param_attribute="ext" /> + </action> + </actions> + </data></outputs><tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: api/history_contents, index: handle hda_dict building exceptions by appending an error-state hda_dict (instead of 'fail-on-first'); history panel: handle bootstrapped and ajax hda api exceptions more gracefully, show hda api exceptions as hdas in the error state.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/50c65739cd1a/ changeset: 50c65739cd1a user: carlfeberhard date: 2013-01-18 22:32:05 summary: api/history_contents, index: handle hda_dict building exceptions by appending an error-state hda_dict (instead of 'fail-on-first'); history panel: handle bootstrapped and ajax hda api exceptions more gracefully, show hda api exceptions as hdas in the error state. affected #: 4 files diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -60,8 +60,20 @@ # but we(I?) need an hda collection with full data somewhere ids = ids.split( ',' ) for hda in history.datasets: - if trans.security.encode_id( hda.id ) in ids: - rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + #TODO: curr. ordered by history, change to order from ids list + encoded_hda_id = trans.security.encode_id( hda.id ) + if encoded_hda_id in ids: + #TODO: share code with show + try: + rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + + except Exception, exc: + # don't fail entire list if hda err's, record and move on + # (making sure http recvr knows it's err'd) + trans.response.status = 500 + log.error( "Error in history API at listing contents " + + "with history %s, hda %s: %s", history_id, encoded_hda_id, str( exc ) ) + rval.append( self._exception_as_hda_dict( trans, encoded_hda_id, exc ) ) else: # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history @@ -69,12 +81,14 @@ rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: - rval = "Error in history API at listing contents" + # for errors that are not specific to one hda (history lookup or summary list) + rval = "Error in history API at listing contents: " + str( e ) log.error( rval + ": %s, %s" % ( type( e ), str( e ) ) ) trans.response.status = 500 return rval + #TODO: move to model or Mixin def _summary_hda_dict( self, trans, history_id, hda ): """ Returns a dictionary based on the HDA in .. _summary form:: @@ -94,6 +108,26 @@ 'url' : url_for( 'history_content', history_id=history_id, id=encoded_id, ), } + #TODO: move to model or Mixin + def _exception_as_hda_dict( self, trans, hda_id, exception ): + """ + Returns a dictionary for an HDA that raised an exception when it's + dictionary was being built. + { + 'id' : < the encoded dataset id >, + 'type' : < name of the dataset >, + 'url' : < api url to retrieve this datasets full data >, + } + """ + return { + 'id' : hda_id, + 'state' : trans.app.model.Dataset.states.ERROR, + 'visible' : True, + 'misc_info' : str( exception ), + 'misc_blurb': 'Failed to retrieve dataset information.', + 'error' : str( exception ) + } + @web.expose_api def show( self, trans, id, history_id, **kwd ): """ diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -445,7 +445,7 @@ if( !this.model.get( 'purged' ) ){ parent.append( $( '<div>' + this.model.get( 'misc_blurb' ) + '</div>' ) ); } - parent.append( ( _l( 'An error occurred running this job' ) + ': ' + parent.append( ( _l( 'An error occurred with this dataset' ) + ': ' + '<i>' + $.trim( this.model.get( 'misc_info' ) ) + '</i>' ) ); parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers.concat([ this._render_downloadButton ]) diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -55,9 +55,17 @@ this.hdas = new HDACollection(); // if we've got hdas passed in the constructor, load them and set up updates if needed - if( initialHdas && initialHdas.length ){ - this.hdas.reset( initialHdas ); - this.checkForUpdates(); + if( initialHdas ){ + if( _.isArray( initialHdas ) ){ + this.hdas.reset( initialHdas ); + this.checkForUpdates(); + + // handle errors in initialHdas + //TODO: errors from the api shouldn't be plain strings... + //TODO: remove when mappers and hda_dict are unified (or move to alt history) + } else if( _.isString( initialHdas ) && ( initialHdas.match( /error/i ) ) ){ + alert( _l( 'Error loading bootstrapped history' ) + ':\n' + initialHdas ); + } } // events @@ -163,7 +171,7 @@ // send the changed ids (if any) to dataset collection to have them fetch their own model changes if( changedIds.length ){ - history.updateHdas( changedIds ); + history.fetchHdaUpdates( changedIds ); } // set up to keep pulling if this history in run/queue state @@ -193,16 +201,37 @@ * 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 ){ + fetchHdaUpdates : function( hdaIds ){ //TODO:?? move to collection? still need proper url var history = this; jQuery.ajax({ url : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }), + /** + * @inner + */ 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(',') ); + if( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ){ return; } + + var errorJson = JSON.parse( xhr.responseText ); + if( _.isArray( errorJson ) ){ + + // just for debugging/reporting purposes + var grouped = _.groupBy( errorJson, function( hdaData ){ + if( _.has( hdaData, 'error' ) ){ return 'errored'; } + return 'ok'; + }); + history.log( 'fetched, errored datasets:', grouped.errored ); + + // the server already formats the error'd hdas in proper hda-model form + // so we're good to send these on + history.updateHdas( errorJson ); + + } else { + var msg = _l( 'ERROR updating hdas from api history contents' ) + ': '; + history.log( msg, hdaIds, xhr, status, error, errorJSON ); + alert( msg + hdaIds.join(',') ); + } }, /** when the proper models for the requested ids are returned, @@ -210,30 +239,41 @@ * @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...:' ); - hdasToAdd.push( hdaData ); - } - }); - if( hdasToAdd.length ){ - history.addHdas( hdasToAdd ); - } + history.log( history + '.fetchHdaUpdates, success:', status, xhr ); + history.updateHdas( hdaDataList ); } }); }, + /** Update the models in the hdas collection from the data given. + * 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 {Object[]} hdaDataList an array of the model data used to update. + */ + updateHdas : function( hdaDataList ){ + var history = this, + // models/views that need to be created + hdasToAdd = []; + history.log( history + '.updateHdas:', hdaDataList ); + + _.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...:' ); + hdasToAdd.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 ){ diff -r 34e42ae792320b1ee2471f11f341ac55445f52e0 -r 50c65739cd1af36f48672a980db378783dffcdd5 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -191,13 +191,19 @@ ##TODO: api/web controllers should use common code, and this section should call that code <%def name="get_history( id )"><% - return trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) + history_json = trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) + #assert isinstance( history, dict ), ( + # 'Bootstrapped history was expecting a dictionary: %s' %( str( history ) ) ) + return history_json %></%def><%def name="get_current_user()"><% - return trans.webapp.api_controllers[ 'users' ].show( trans, 'current' ) + user_json = trans.webapp.api_controllers[ 'users' ].show( trans, 'current' ) + #assert isinstance( hdaDataList, list ), ( + # 'Bootstrapped current user was expecting a dictionary: %s' %( str( user ) ) ) + return user_json %></%def> @@ -207,10 +213,10 @@ if not hdas: return '[]' # rather just use the history.id (wo the datasets), but... - return trans.webapp.api_controllers[ 'history_contents' ].index( - #trans, trans.security.encode_id( history_id ), + hda_json = trans.webapp.api_controllers[ 'history_contents' ].index( trans, trans.security.encode_id( history_id ), ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) ) + return hda_json %></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Filter request params to only those necessary when redirecting to monitor installing tool shed repositories.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/34e42ae79232/ changeset: 34e42ae79232 user: greg date: 2013-01-18 21:46:22 summary: Filter request params to only those necessary when redirecting to monitor installing tool shed repositories. affected #: 1 file diff -r b238d26ca9269aec91e26370348b89ee14c3d1ae -r 34e42ae792320b1ee2471f11f341ac55445f52e0 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 @@ -977,9 +977,10 @@ return trans.show_error_message( 'Invalid repository specified.' ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: + tool_shed_repository_ids = [ repository_id ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', - **kwd ) ) + tool_shed_repository_ids=tool_shed_repository_ids ) ) if repository.can_install and operation == 'install': # Send a request to the tool shed to install the repository. url = suc.url_join( tool_shed_url, 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: Handle long urls when installing and reinstalling tool shed repositories.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b238d26ca926/ changeset: b238d26ca926 user: greg date: 2013-01-18 21:11:39 summary: Handle long urls when installing and reinstalling tool shed repositories. affected #: 2 files diff -r 03d2ce228f7e939871ff5d1d0564eebdda2cbb36 -r b238d26ca9269aec91e26370348b89ee14c3d1ae lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -350,7 +350,7 @@ # Keep the one-to-one mapping between items in 3 lists. created_or_updated_tool_shed_repositories.append( tool_shed_repository ) tool_panel_section_keys.append( tool_panel_section_key ) - filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) + filtered_repo_info_dicts.append( repo_info_dict ) # Build repository dependency relationships even if the user chose to not install repository dependencies. suc.build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message diff -r 03d2ce228f7e939871ff5d1d0564eebdda2cbb36 -r b238d26ca9269aec91e26370348b89ee14c3d1ae 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 @@ -798,24 +798,6 @@ status=status ) ) @web.expose @web.require_admin - def initiate_repository_installation( self, trans, shed_repository_ids, encoded_kwd, reinstalling=False ): - tsr_ids = util.listify( shed_repository_ids ) - tool_shed_repositories = [] - for tsr_id in tsr_ids: - tsr = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) - tool_shed_repositories.append( tsr ) - clause_list = [] - for tsr_id in tsr_ids: - clause_list.append( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( tsr_id ) ) - query = trans.sa_session.query( trans.model.ToolShedRepository ).filter( or_( *clause_list ) ) - return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', - encoded_kwd=encoded_kwd, - query=query, - tool_shed_repositories=tool_shed_repositories, - initiate_repository_installation_ids=shed_repository_ids, - reinstalling=reinstalling ) - @web.expose - @web.require_admin def initiate_tool_dependency_installation( self, trans, tool_dependencies ): """Install specified dependencies for repository tools.""" # Get the tool_shed_repository from one of the tool_dependencies. @@ -1303,7 +1285,7 @@ else: tool_panel_section_key = None tool_section = None - tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] + encoded_repository_ids = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] # Create a one-to-one mapping of tool shed repository id and tool panel section key. All tools contained in the repositories # being installed will be loaded into the same section in the tool panel. for tsr in created_or_updated_tool_shed_repositories: @@ -1319,15 +1301,24 @@ status=status, tool_path=tool_path, tool_panel_section_keys=tool_panel_section_keys, - tool_shed_repository_ids=tsrids_list, + tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) - tsrids_str = ','.join( tsrids_list ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='initiate_repository_installation', - shed_repository_ids=tsrids_str, - encoded_kwd=encoded_kwd, - reinstalling=False ) ) + tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ] + tool_shed_repositories = [] + for tsr_id in tsr_ids: + tsr = trans.sa_session.query( trans.model.ToolShedRepository ).get( tsr_id ) + tool_shed_repositories.append( tsr ) + clause_list = [] + for tsr_id in tsr_ids: + clause_list.append( trans.model.ToolShedRepository.table.c.id == tsr_id ) + query = trans.sa_session.query( trans.model.ToolShedRepository ).filter( or_( *clause_list ) ) + return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', + encoded_kwd=encoded_kwd, + query=query, + tool_shed_repositories=tool_shed_repositories, + initiate_repository_installation_ids=encoded_repository_ids, + reinstalling=False ) else: kwd[ 'message' ] = message kwd[ 'status' ] = status @@ -1516,11 +1507,21 @@ tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='initiate_repository_installation', - shed_repository_ids=encoded_repository_ids, - encoded_kwd=encoded_kwd, - reinstalling=True ) ) + tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ] + tool_shed_repositories = [] + for tsr_id in tsr_ids: + tsr = trans.sa_session.query( trans.model.ToolShedRepository ).get( tsr_id ) + tool_shed_repositories.append( tsr ) + clause_list = [] + for tsr_id in tsr_ids: + clause_list.append( trans.model.ToolShedRepository.table.c.id == tsr_id ) + query = trans.sa_session.query( trans.model.ToolShedRepository ).filter( or_( *clause_list ) ) + return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', + encoded_kwd=encoded_kwd, + query=query, + tool_shed_repositories=tool_shed_repositories, + initiate_repository_installation_ids=encoded_repository_ids, + reinstalling=True ) @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Cloud Launch: Adjust event triggers to prevent redundant (though harmless) get_account_info invocations. Change get_account_info to POST vs GET. Adjust Cluster List creation to *always* insert the "New Cluster" option. Prevent nonexisting existing instance value from crashing zone detection during submission.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/03d2ce228f7e/ changeset: 03d2ce228f7e user: dannon date: 2013-01-18 20:38:51 summary: Cloud Launch: Adjust event triggers to prevent redundant (though harmless) get_account_info invocations. Change get_account_info to POST vs GET. Adjust Cluster List creation to *always* insert the "New Cluster" option. Prevent nonexisting existing instance value from crashing zone detection during submission. affected #: 1 file diff -r 98f724202d9d3cea035d7de04d89465bcf3092b1 -r 03d2ce228f7e939871ff5d1d0564eebdda2cbb36 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -76,22 +76,24 @@ } }); //When id_secret and id_key are complete, submit to get_account_info - $("#id_secret, #id_key_id").bind("change paste keyup input propertychange", function(){ + $("#id_secret, #id_key_id").bind("paste input propertychange", function(){ secret_el = $("#id_secret"); key_el = $("#id_key_id"); if (secret_el.val().length === 40 && key_el.val().length === 20){ //Submit these to get_account_info, unhide fields, and update as appropriate - $.getJSON(ACCOUNT_URL, - {key_id: key_el.val(),secret:secret_el.val()}, - function(result){ + $.ajax({type: "POST", + url: ACCOUNT_URL, + dataType: 'json', + data: {key_id: key_el.val(),secret:secret_el.val()}, + success: function(result){ cloudlaunch_clusters = result.clusters; var kplist = $("#id_keypair"); var clusterlist = $("#id_existing_instance"); kplist.find('option').remove(); clusterlist.find('option').remove(); //Update fields with appropriate elements + clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); if (_.size(result.clusters) > 0){ - clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); _.each(result.clusters, function(cluster, index){ clusterlist.append($('<option/>').val(cluster.name).text(cluster.name)); }); @@ -104,7 +106,8 @@ kplist.append($('<option/>').val(keypair).text(keypair)); }); $('#hidden_options').show('fast'); - }); + } + }); } }); $('#loading_indicator').ajaxStart(function(){ @@ -130,7 +133,7 @@ //Dig up zone info for selected cluster, set hidden input. //This is not necessary to present to the user though the interface may prove useful. var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'}); - if( ei_val.value !== "New Cluster"){ + if( ei_val && (ei_val.value !== "New Cluster")){ var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value}); var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'}); zdata.value = cluster.zone; 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: 3 new changesets
by Bitbucket 18 Jan '13

18 Jan '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6aef91d12890/ changeset: 6aef91d12890 user: kellrott date: 2012-12-27 20:40:20 summary: The start of the API based annotation system affected #: 3 files diff -r c8f0ea550d51b2c203f5f60568817164c62220fd -r 6aef91d128904c405356e9fa2f3afa43368c8e8a lib/galaxy/model/item_attrs.py --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -137,6 +137,12 @@ # Set annotation. annotation_assoc.annotation = annotation return annotation_assoc + + def delete_item_annotation( self, db_session, user, item): + annotation_assoc = self.get_item_annotation_obj( db_session, user, item ) + if annotation_assoc: + db_session.delete(annotation_assoc) + db_session.flush() def copy_item_annotation( self, db_session, source_user, source_item, target_user, target_item ): """ Copy an annotation from a user/item source to a user/item target. """ diff -r c8f0ea550d51b2c203f5f60568817164c62220fd -r 6aef91d128904c405356e9fa2f3afa43368c8e8a lib/galaxy/webapps/galaxy/api/annotations.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -0,0 +1,76 @@ +""" +API operations on annotations. +""" +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.model.item_attrs import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * +import galaxy.datatypes +from galaxy.util.bunch import Bunch + +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + +log = logging.getLogger( __name__ ) + +class BaseAnnotationsController( BaseAPIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ): + + @web.expose_api + def index( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.get_item_annotation_str( trans.sa_session, trans.get_user(), item ) + + + @web.expose_api + def create( self, trans, payload, **kwd ): + if "text" not in payload: + return "" + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + new_annotation = payload.get("text") + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) + + self.add_item_annotation( trans.sa_session, trans.get_user(), item, new_annotation ) + trans.sa_session.flush() + return new_annotation + return "" + + @web.expose_api + def delete( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.delete_item_annotation( trans.sa_session, trans.get_user(), item ) + + @web.expose_api + def undelete( self, trans, **kwd ): + raise HTTPNotImplemented() + +class HistoryAnnotationsController(BaseAnnotationsController): + controller_name = "history_annotations" + tagged_item_id = "history_id" + def _get_item_from_id(self, trans, idstr): + hist = self.get_history( trans, idstr ) + return hist + +class HistoryContentAnnotationsController(BaseAnnotationsController): + controller_name = "history_content_annotations" + tagged_item_id = "history_content_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_dataset(trans, idstr) + return hda + +class WorkflowAnnotationsController(BaseAnnotationsController): + controller_name = "workflow_annotations" + tagged_item_id = "workflow_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_stored_workflow(trans, idstr) + return hda diff -r c8f0ea550d51b2c203f5f60568817164c62220fd -r 6aef91d128904c405356e9fa2f3afa43368c8e8a lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -105,6 +105,17 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) + + _add_item_annotation_controller( webapp, + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + _add_item_annotation_controller( webapp, + name_prefix="history_", + path_prefix='/api/histories/:history_id' ) + _add_item_annotation_controller( webapp, + name_prefix="workflow_", + path_prefix='/api/workflows/:workflow_id' ) + webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -185,6 +196,12 @@ conditions=dict(method=["GET"])) + +def _add_item_annotation_controller( webapp, name_prefix, path_prefix, **kwd ): + controller = "%sannotations" % name_prefix + name = "%sannotation" % name_prefix + webapp.api_mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) + def wrap_in_middleware( app, global_conf, **local_conf ): """ Based on the configuration wrap `app` in a set of common and useful https://bitbucket.org/galaxy/galaxy-central/commits/f8fac0ad9808/ changeset: f8fac0ad9808 user: kellrott date: 2013-01-18 17:52:33 summary: Removing '*' imports from annotations API module affected #: 1 file diff -r 6aef91d128904c405356e9fa2f3afa43368c8e8a -r f8fac0ad9808825e4ac7228a9da5e0f8d8a3ca48 lib/galaxy/webapps/galaxy/api/annotations.py --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -4,10 +4,9 @@ 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.model.item_attrs import * +from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin +from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * import galaxy.datatypes from galaxy.util.bunch import Bunch https://bitbucket.org/galaxy/galaxy-central/commits/98f724202d9d/ changeset: 98f724202d9d user: jgoecks date: 2013-01-18 18:02:51 summary: Merged in kellrott/galaxy-central (pull request #101) The start of the API based annotation system affected #: 3 files diff -r 666d744054ded20d79e3d2c6eb65012455de96b5 -r 98f724202d9d3cea035d7de04d89465bcf3092b1 lib/galaxy/model/item_attrs.py --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -137,6 +137,12 @@ # Set annotation. annotation_assoc.annotation = annotation return annotation_assoc + + def delete_item_annotation( self, db_session, user, item): + annotation_assoc = self.get_item_annotation_obj( db_session, user, item ) + if annotation_assoc: + db_session.delete(annotation_assoc) + db_session.flush() def copy_item_annotation( self, db_session, source_user, source_item, target_user, target_item ): """ Copy an annotation from a user/item source to a user/item target. """ diff -r 666d744054ded20d79e3d2c6eb65012455de96b5 -r 98f724202d9d3cea035d7de04d89465bcf3092b1 lib/galaxy/webapps/galaxy/api/annotations.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -0,0 +1,75 @@ +""" +API operations on annotations. +""" +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 BaseAPIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.util.sanitize_html import sanitize_html +import galaxy.datatypes +from galaxy.util.bunch import Bunch + +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + +log = logging.getLogger( __name__ ) + +class BaseAnnotationsController( BaseAPIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ): + + @web.expose_api + def index( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.get_item_annotation_str( trans.sa_session, trans.get_user(), item ) + + + @web.expose_api + def create( self, trans, payload, **kwd ): + if "text" not in payload: + return "" + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + new_annotation = payload.get("text") + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) + + self.add_item_annotation( trans.sa_session, trans.get_user(), item, new_annotation ) + trans.sa_session.flush() + return new_annotation + return "" + + @web.expose_api + def delete( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.delete_item_annotation( trans.sa_session, trans.get_user(), item ) + + @web.expose_api + def undelete( self, trans, **kwd ): + raise HTTPNotImplemented() + +class HistoryAnnotationsController(BaseAnnotationsController): + controller_name = "history_annotations" + tagged_item_id = "history_id" + def _get_item_from_id(self, trans, idstr): + hist = self.get_history( trans, idstr ) + return hist + +class HistoryContentAnnotationsController(BaseAnnotationsController): + controller_name = "history_content_annotations" + tagged_item_id = "history_content_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_dataset(trans, idstr) + return hda + +class WorkflowAnnotationsController(BaseAnnotationsController): + controller_name = "workflow_annotations" + tagged_item_id = "workflow_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_stored_workflow(trans, idstr) + return hda diff -r 666d744054ded20d79e3d2c6eb65012455de96b5 -r 98f724202d9d3cea035d7de04d89465bcf3092b1 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -107,6 +107,17 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) + + _add_item_annotation_controller( webapp, + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + _add_item_annotation_controller( webapp, + name_prefix="history_", + path_prefix='/api/histories/:history_id' ) + _add_item_annotation_controller( webapp, + name_prefix="workflow_", + path_prefix='/api/workflows/:workflow_id' ) + webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -193,6 +204,12 @@ conditions=dict(method=["GET"])) + +def _add_item_annotation_controller( webapp, name_prefix, path_prefix, **kwd ): + controller = "%sannotations" % name_prefix + name = "%sannotation" % name_prefix + webapp.api_mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) + def wrap_in_middleware( app, global_conf, **local_conf ): """ Based on the configuration wrap `app` in a set of common and useful Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Readd add/remove buttons' HTML element class names that was omitted due to a poor merge of pull request #24.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/666d744054de/ changeset: 666d744054de user: jgoecks date: 2013-01-18 17:59:11 summary: Readd add/remove buttons' HTML element class names that was omitted due to a poor merge of pull request #24. affected #: 1 file diff -r a0db2696ba21ff636d3fd75699fe995c0e8c2262 -r 666d744054ded20d79e3d2c6eb65012455de96b5 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -151,7 +151,7 @@ <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} %if input.min < num_repeats: - <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> %endif </div> %if rep_errors.has_key( '__index__' ): @@ -159,7 +159,7 @@ %endif %endfor %if input.max > num_repeats: - <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> %endif </div> %elif input.type == "conditional": 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: inithello: Removed hg merge conflict markers.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0db2696ba21/ changeset: a0db2696ba21 user: inithello date: 2013-01-18 17:42:35 summary: Removed hg merge conflict markers. affected #: 1 file diff -r 864e960c52474fe6cb19129196b0ccccf48856bd -r a0db2696ba21ff636d3fd75699fe995c0e8c2262 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -150,25 +150,17 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} -<<<<<<< local - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> -======= %if input.min < num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> %endif ->>>>>>> other </div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor -<<<<<<< local - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> -======= %if input.max > num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> %endif ->>>>>>> other </div> %elif input.type == "conditional": <% 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: Tool shed import fixes.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/864e960c5247/ changeset: 864e960c5247 user: greg date: 2013-01-18 17:40:29 summary: Tool shed import fixes. affected #: 7 files diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -1,9 +1,9 @@ -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController +from galaxy import web, util from galaxy.web.base.controllers.admin import Admin from galaxy.webapps.community import model from galaxy.model.orm import and_ -from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.web.form_builder import SelectField +from galaxy.web.framework.helpers import time_ago, grids from galaxy.util import inflector import galaxy.util.shed_util_common as suc from repository import RepositoryGrid, CategoryGrid diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,10 +1,6 @@ import logging from galaxy.model.item_attrs import UsesItemRatings -from galaxy import eggs -eggs.require('mercurial') -from mercurial import hg, ui, commands - log = logging.getLogger( __name__ ) class ItemRatings( UsesItemRatings ): diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -1,5 +1,6 @@ import os, logging -from galaxy.web.base.controller import * +from galaxy import web +from galaxy.web.base.controller import BaseUIController from galaxy.util.shed_util_common import get_repository_by_name_and_owner, set_repository_metadata from galaxy import eggs diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -1,9 +1,9 @@ import os, logging -from galaxy import util -from galaxy.web.base.controller import * +from galaxy import web, util +from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import SelectField, CheckboxField from galaxy.webapps.community import model -from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_ from sqlalchemy.sql.expression import func import common diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -1,5 +1,6 @@ import sys, os, shutil, logging, tarfile, tempfile, urllib -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController +from galaxy import web, util from galaxy.datatypes import checkers import galaxy.util.shed_util_common as suc diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/framework/middleware/hg.py --- a/lib/galaxy/webapps/community/framework/middleware/hg.py +++ b/lib/galaxy/webapps/community/framework/middleware/hg.py @@ -2,7 +2,7 @@ Middleware for handling hg authentication for users pushing change sets to local repositories. """ import os, logging -from sqlalchemy import * +import sqlalchemy from paste.auth.basic import AuthBasicAuthenticator from paste.httpheaders import REMOTE_USER, AUTH_TYPE @@ -43,7 +43,7 @@ username = path_info_components[1] name = path_info_components[2] # Instantiate a database connection - engine = create_engine( self.db_url ) + engine = sqlalchemy.create_engine( self.db_url ) connection = engine.connect() result_set = connection.execute( "select id from galaxy_user where username = '%s'" % username.lower() ) for row in result_set: @@ -101,7 +101,7 @@ return self.__authenticate( username, password ) def __authenticate( self, username, password ): # Instantiate a database connection - engine = create_engine( self.db_url ) + engine = sqlalchemy.create_engine( self.db_url ) connection = engine.connect() result_set = connection.execute( "select email, password from galaxy_user where username = '%s'" % username.lower() ) for row in result_set: diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd 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 @@ -1,15 +1,24 @@ -import urllib2, tempfile -from admin import * +import logging, os, shutil, tempfile, urllib2 +from admin import AdminGalaxy +from galaxy import model, web, util +from galaxy.web.form_builder import SelectField, CheckboxField +from galaxy.web.framework.helpers import iff, grids from galaxy.util import json +from galaxy.model.orm import or_ import galaxy.util.shed_util as shed_util import galaxy.util.shed_util_common as suc from galaxy.tool_shed import encoding_util from galaxy.webapps.community.util import container_util, workflow_util from galaxy import eggs, tools +import pkg_resources eggs.require( 'mercurial' ) from mercurial import hg, ui, commands +pkg_resources.require( 'elementtree' ) +from elementtree import ElementTree +from elementtree.ElementTree import Element + log = logging.getLogger( __name__ ) class InstalledRepositoryGrid( grids.Grid ): @@ -447,7 +456,7 @@ @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = url_for( '/', qualified=True ) + galaxy_url = web.url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) ) return trans.response.send_redirect( url ) @web.expose @@ -469,7 +478,7 @@ tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) url = suc.url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ - ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) + ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -557,14 +566,14 @@ @web.require_admin def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = url_for( '/', qualified=True ) + galaxy_url = web.url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = url_for( '/', qualified=True ) + galaxy_url = web.url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @@ -993,7 +1002,7 @@ # Send a request to the tool shed to install the repository. url = suc.url_join( tool_shed_url, 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ - ( repository.name, repository.owner, repository.installed_changeset_revision, ( url_for( '/', qualified=True ) ) ) ) + ( repository.name, repository.owner, repository.installed_changeset_revision, ( web.url_for( '/', qualified=True ) ) ) ) return trans.response.send_redirect( url ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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