[galaxy-commits] commit/galaxy-central: greg: Utility refactoring cleanu and import tweaks.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c0c6cf9f5d6e/ changeset: c0c6cf9f5d6e user: greg date: 2012-12-13 16:14:01 summary: Utility refactoring cleanu and import tweaks. affected #: 6 files diff -r 70f88a048ed2b565d60250ca66302fd03a7852ff -r c0c6cf9f5d6ee0a63d0c058439467c1340698930 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -5,7 +5,7 @@ import urllib2, tempfile from galaxy.tools import ToolSection from galaxy.util.json import from_json_string, to_json_string -from galaxy.util.shed_util import * +import galaxy.util.shed_util as shed_util import galaxy.util.shed_util_common as suc from galaxy.util.odict import odict from galaxy.tool_shed.common_util import * @@ -36,9 +36,9 @@ self.tool_shed_install_config = tool_shed_install_config tree = util.parse_xml( tool_shed_install_config ) root = tree.getroot() - self.tool_shed = clean_tool_shed_url( root.get( 'name' ) ) + self.tool_shed = shed_util.clean_tool_shed_url( root.get( 'name' ) ) self.repository_owner = REPOSITORY_OWNER - index, self.shed_config_dict = get_shed_tool_conf_dict( app, self.migrated_tools_config ) + index, self.shed_config_dict = shed_util.get_shed_tool_conf_dict( app, self.migrated_tools_config ) # Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in # tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk. # The default behavior is that the tool shed is down. @@ -172,7 +172,7 @@ # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) if is_displayed: - tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) + tool_panel_dict_for_tool_config = shed_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v else: @@ -192,50 +192,50 @@ self.app.sa_session.flush() if 'tool_dependencies' in metadata_dict: # All tool_dependency objects must be created before the tools are processed even if no tool dependencies will be installed. - tool_dependencies = create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) + tool_dependencies = shed_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) else: tool_dependencies = None if 'tools' in metadata_dict: sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = get_tool_index_sample_files( sample_files ) - copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) + tool_index_sample_files = shed_util.get_tool_index_sample_files( sample_files ) + shed_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = get_repository_tools_tups( self.app, metadata_dict ) + repository_tools_tups = shed_util.get_repository_tools_tups( self.app, metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups ) + repository_tools_tups = shed_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups ) # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups, sample_files_copied = handle_missing_index_file( self.app, - self.tool_path, - sample_files, - repository_tools_tups, - sample_files_copied ) + repository_tools_tups, sample_files_copied = shed_util.handle_missing_index_file( self.app, + self.tool_path, + sample_files, + repository_tools_tups, + sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied ) + shed_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied ) if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict: # Install tool dependencies. - update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + shed_util.update_tool_shed_repository_status( self.app, + tool_shed_repository, + self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) - installed_tool_dependencies = handle_tool_dependencies( app=self.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies ) + installed_tool_dependencies = shed_util.handle_tool_dependencies( app=self.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.model.ToolDependency.installation_status.ERROR: print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - add_to_tool_panel( self.app, - tool_shed_repository.name, - repository_clone_url, - tool_shed_repository.installed_changeset_revision, - repository_tools_tups, - self.repository_owner, - self.migrated_tools_config, - tool_panel_dict=tool_panel_dict_for_display, - new_install=True ) + shed_util.add_to_tool_panel( self.app, + tool_shed_repository.name, + repository_clone_url, + tool_shed_repository.installed_changeset_revision, + repository_tools_tups, + self.repository_owner, + self.migrated_tools_config, + tool_panel_dict=tool_panel_dict_for_display, + new_install=True ) if 'datatypes' in metadata_dict: tool_shed_repository.status = self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -246,16 +246,16 @@ datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', repo_install_dir ) # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started # after this installation completes. - converter_path, display_path = alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir + converter_path, display_path = shed_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir if converter_path or display_path: # Create a dictionary of tool shed repository related information. - repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, - name=tool_shed_repository.name, - owner=self.repository_owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) + repository_dict = shed_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, + name=tool_shed_repository.name, + owner=self.repository_owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict ) @@ -281,20 +281,20 @@ repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) - ctx_rev = get_ctx_rev( tool_shed_url, name, self.repository_owner, installed_changeset_revision ) + ctx_rev = shed_util.get_ctx_rev( tool_shed_url, name, self.repository_owner, installed_changeset_revision ) print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name - tool_shed_repository = create_or_update_tool_shed_repository( app=self.app, - name=name, - description=description, - installed_changeset_revision=installed_changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=self.app.model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=None, - owner=self.repository_owner, - dist_to_shed=True ) - update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) + tool_shed_repository = shed_util.create_or_update_tool_shed_repository( app=self.app, + name=name, + description=description, + installed_changeset_revision=installed_changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=self.app.model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=None, + owner=self.repository_owner, + dist_to_shed=True ) + shed_util.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, @@ -305,9 +305,9 @@ self.app.sa_session.refresh( tool_shed_repository ) metadata_dict = tool_shed_repository.metadata if 'tools' in metadata_dict: - update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + shed_util.update_tool_shed_repository_status( self.app, + tool_shed_repository, + self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) # Get the tool_versions from the tool shed for each tool in the installed change set. url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) @@ -316,7 +316,7 @@ response.close() if text: tool_version_dicts = from_json_string( text ) - handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) + shed_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) else: # Set the tool versions since they seem to be missing for this repository in the tool shed. # CRITICAL NOTE: These default settings may not properly handle all parent/child associations. @@ -325,8 +325,8 @@ tool_id = tool_dict[ 'guid' ] old_tool_id = tool_dict[ 'id' ] tool_version = tool_dict[ 'version' ] - tool_version_using_old_id = get_tool_version( self.app, old_tool_id ) - tool_version_using_guid = get_tool_version( self.app, tool_id ) + tool_version_using_old_id = shed_util.get_tool_version( self.app, old_tool_id ) + tool_version_using_guid = shed_util.get_tool_version( self.app, tool_id ) if not tool_version_using_old_id: tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id, tool_shed_repository=tool_shed_repository ) @@ -338,15 +338,15 @@ self.app.sa_session.add( tool_version_using_guid ) self.app.sa_session.flush() # Associate the two versions as parent / child. - tool_version_association = get_tool_version_association( self.app, - tool_version_using_old_id, - tool_version_using_guid ) + tool_version_association = shed_util.get_tool_version_association( self.app, + tool_version_using_old_id, + tool_version_using_guid ) if not tool_version_association: tool_version_association = self.app.model.ToolVersionAssociation( tool_id=tool_version_using_guid.id, parent_id=tool_version_using_old_id.id ) self.app.sa_session.add( tool_version_association ) self.app.sa_session.flush() - update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED ) + shed_util.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED ) @property def non_shed_tool_panel_configs( self ): return get_non_shed_tool_panel_configs( self.app ) diff -r 70f88a048ed2b565d60250ca66302fd03a7852ff -r c0c6cf9f5d6ee0a63d0c058439467c1340698930 lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -3,7 +3,7 @@ """ import threading, urllib2, logging from galaxy.util import string_as_bool -from galaxy.util.shed_util import * +import galaxy.util.shed_util as shed_util log = logging.getLogger( __name__ ) diff -r 70f88a048ed2b565d60250ca66302fd03a7852ff -r c0c6cf9f5d6ee0a63d0c058439467c1340698930 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -32,7 +32,7 @@ from cgi import FieldStorage from galaxy.util.hash_util import * from galaxy.util import listify -from galaxy.util.shed_util import * +import galaxy.util.shed_util as shed_util from galaxy.web import url_for from galaxy.visualization.genome.visual_analytics import TracksterConfig @@ -887,11 +887,11 @@ def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. if self.tool_shed: - return get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, - self.tool_shed, - self.repository_name, - self.repository_owner, - self.installed_changeset_revision ) + return shed_util.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, + self.tool_shed, + self.repository_name, + self.repository_owner, + self.installed_changeset_revision ) return None def __get_job_run_config( self, run_configs, key, job_params=None ): # Look through runners/handlers to find one with matching parameters. diff -r 70f88a048ed2b565d60250ca66302fd03a7852ff -r c0c6cf9f5d6ee0a63d0c058439467c1340698930 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,4 +1,5 @@ import os, tempfile, shutil, logging, urllib2 +from galaxy.datatypes import checkers from galaxy import util import shed_util_common as suc from galaxy.tools.search import ToolBoxSearch @@ -293,10 +294,6 @@ set_status=set_status ) tool_dependency_objects.append( tool_dependency ) return tool_dependency_objects -def generate_clone_url_for_installed_repository( trans, repository ): - """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) - return suc.url_join( tool_shed_url, 'repos', repository.owner, repository.name ) 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' ) @@ -542,9 +539,6 @@ if idx == count: break return headers -def get_installed_tool_shed_repository( trans, id ): - """Get a repository on the Galaxy side from the database via id""" - return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) def get_repository_owner( cleaned_repository_url ): items = cleaned_repository_url.split( 'repos' ) repo_path = items[ 1 ] @@ -1042,44 +1036,6 @@ trans.sa_session.add( tool_dependency ) trans.sa_session.flush() return removed, error_message -def tool_shed_from_repository_clone_url( repository_clone_url ): - return suc.clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) -def update_in_shed_tool_config( app, repository ): - # A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list - # of config_elems instead of using the in-memory list. - shed_conf_dict = repository.get_shed_config_dict( app ) - shed_tool_conf = shed_conf_dict[ 'config_filename' ] - tool_path = shed_conf_dict[ 'tool_path' ] - - #hack for 'trans.app' used in lots of places. These places should just directly use app - trans = util.bunch.Bunch() - trans.app = app - - tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) - repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) - cleaned_repository_clone_url = suc.clean_repository_clone_url( generate_clone_url_for_installed_repository( trans, repository ) ) - tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner - if not owner: - owner = get_repository_owner( cleaned_repository_clone_url ) - guid_to_tool_elem_dict = {} - for tool_config_filename, guid, tool in repository_tools_tups: - guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) - config_elems = [] - tree = util.parse_xml( shed_tool_conf ) - root = tree.getroot() - for elem in root: - if elem.tag == 'section': - for i, tool_elem in enumerate( elem ): - guid = tool_elem.attrib.get( 'guid' ) - if guid in guid_to_tool_elem_dict: - elem[i] = guid_to_tool_elem_dict[ guid ] - elif elem.tag == 'tool': - guid = elem.attrib.get( 'guid' ) - if guid in guid_to_tool_elem_dict: - elem = guid_to_tool_elem_dict[ guid ] - config_elems.append( elem ) - config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) def update_tool_shed_repository_status( app, tool_shed_repository, status ): sa_session = app.model.context.current tool_shed_repository.status = status diff -r 70f88a048ed2b565d60250ca66302fd03a7852ff -r c0c6cf9f5d6ee0a63d0c058439467c1340698930 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -565,6 +565,10 @@ repository_dependencies, metadata.get( 'tool_dependencies', None ) ) return repo_info_dict +def generate_clone_url_for_installed_repository( trans, repository ): + """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" + tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + return suc.url_join( tool_shed_url, 'repos', repository.owner, repository.name ) def generate_clone_url_for_repository_in_tool_shed( trans, repository ): """Generate the URL for cloning a repository that is in the tool shed.""" base_url = url_for( '/', qualified=True ).rstrip( '/' ) @@ -1056,6 +1060,9 @@ if deleted: return 'DELETED' return None +def get_installed_tool_shed_repository( trans, id ): + """Get a repository on the Galaxy side from the database via id""" + return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) def get_list_of_copied_sample_files( repo, ctx, dir ): """ Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy @@ -2011,6 +2018,8 @@ if to_html: str( markupsafe.escape( ''.join( translated ) ) ) return ''.join( translated ) +def tool_shed_from_repository_clone_url( repository_clone_url ): + return suc.clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def tool_shed_is_this_tool_shed( toolshed_base_url ): return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' ) def translate_string( raw_text, to_html=True ): @@ -2090,6 +2099,42 @@ sa_session.delete( tool_dependency ) sa_session.flush() return new_tool_dependency +def update_in_shed_tool_config( app, repository ): + # A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list + # of config_elems instead of using the in-memory list. + shed_conf_dict = repository.get_shed_config_dict( app ) + shed_tool_conf = shed_conf_dict[ 'config_filename' ] + tool_path = shed_conf_dict[ 'tool_path' ] + + #hack for 'trans.app' used in lots of places. These places should just directly use app + trans = util.bunch.Bunch() + trans.app = app + + tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) + repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) + cleaned_repository_clone_url = suc.clean_repository_clone_url( suc.generate_clone_url_for_installed_repository( trans, repository ) ) + tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) + owner = repository.owner + if not owner: + owner = get_repository_owner( cleaned_repository_clone_url ) + guid_to_tool_elem_dict = {} + for tool_config_filename, guid, tool in repository_tools_tups: + guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) + config_elems = [] + tree = util.parse_xml( shed_tool_conf ) + root = tree.getroot() + for elem in root: + if elem.tag == 'section': + for i, tool_elem in enumerate( elem ): + guid = tool_elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem[i] = guid_to_tool_elem_dict[ guid ] + elif elem.tag == 'tool': + guid = elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem = guid_to_tool_elem_dict[ guid ] + config_elems.append( elem ) + config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) def update_repository( repo, ctx_rev=None ): """ Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired diff -r 70f88a048ed2b565d60250ca66302fd03a7852ff -r c0c6cf9f5d6ee0a63d0c058439467c1340698930 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 @@ -1,7 +1,7 @@ import urllib2, tempfile from admin import * from galaxy.util.json import from_json_string, to_json_string -from galaxy.util.shed_util import * +import galaxy.util.shed_util as shed_util import galaxy.util.shed_util_common as suc from galaxy.tool_shed.encoding_util import * from galaxy import eggs, tools @@ -284,7 +284,7 @@ model.ToolDependency.installation_status.ERROR ] ) ) ] def build_initial_query( self, trans, **kwd ): - tool_dependency_ids = get_tool_dependency_ids( as_string=False, **kwd ) + tool_dependency_ids = shed_util.get_tool_dependency_ids( as_string=False, **kwd ) if tool_dependency_ids: clause_list = [] for tool_dependency_id in tool_dependency_ids: @@ -308,15 +308,15 @@ @web.require_admin def activate_repository( self, trans, **kwd ): """Activate a repository that was deactivated but not uninstalled.""" - repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) - shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - repository_clone_url = generate_clone_url_for_installed_repository( trans, repository ) + repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + shed_tool_conf, tool_path, relative_install_dir = shed_util.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans, repository ) repository.deleted = False repository.status = trans.model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools: metadata = repository.metadata try: - repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + repository_tools_tups = shed_util.get_repository_tools_tups( trans.app, metadata ) except Exception, e: error = "Error activating repository %s: %s" % ( repository.name, str( e ) ) log.debug( error ) @@ -324,25 +324,25 @@ % ( error, web.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) ) ) ) # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] - add_to_tool_panel( trans.app, - repository.name, - repository_clone_url, - repository.changeset_revision, - repository_tools_tups, - repository.owner, - shed_tool_conf, - tool_panel_dict, - new_install=False ) + shed_util.add_to_tool_panel( trans.app, + repository.name, + repository_clone_url, + repository.changeset_revision, + repository_tools_tups, + repository.owner, + shed_tool_conf, + tool_panel_dict, + new_install=False ) trans.sa_session.add( repository ) trans.sa_session.flush() if repository.includes_datatypes: repository_install_dir = os.path.abspath ( relative_install_dir ) # Deactivate proprietary datatypes. - installed_repository_dict = load_installed_datatypes( trans.app, repository, repository_install_dir, deactivate=False ) + installed_repository_dict = shed_util.load_installed_datatypes( trans.app, repository, repository_install_dir, deactivate=False ) if installed_repository_dict and 'converter_path' in installed_repository_dict: - load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=False ) + shed_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=False ) if installed_repository_dict and 'display_path' in installed_repository_dict: - load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False ) + shed_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False ) message = 'The <b>%s</b> repository has been activated.' % repository.name status = 'done' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -355,7 +355,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', repository=repository, message=message, @@ -379,7 +379,7 @@ action='reset_to_install', **kwd ) ) if operation == "activate or reinstall": - repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: if repository.includes_tools: # Only allow selecting a different section in the tool panel if the repository was uninstalled. @@ -407,7 +407,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - tool_dependency = get_tool_dependency( trans, kwd[ 'id' ] ) + tool_dependency = shed_util.get_tool_dependency( trans, kwd[ 'id' ] ) if tool_dependency.in_error_state: message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). " message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems " @@ -439,7 +439,7 @@ @web.require_admin def check_for_updates( self, trans, **kwd ): # Send a request to the relevant tool shed to see if there are any updates. - repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) 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' % \ @@ -459,8 +459,8 @@ status = params.get( 'status', 'done' ) remove_from_disk = params.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) - tool_shed_repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) - shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + shed_tool_conf, tool_path, relative_install_dir = shed_util.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) if relative_install_dir: if tool_path: relative_install_dir = os.path.join( tool_path, relative_install_dir ) @@ -471,14 +471,14 @@ if params.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools: # Handle tool panel alterations. - remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) + shed_util.remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_datatypes: # Deactivate proprietary datatypes. - installed_repository_dict = load_installed_datatypes( trans.app, tool_shed_repository, repository_install_dir, deactivate=True ) + installed_repository_dict = shed_util.load_installed_datatypes( trans.app, tool_shed_repository, repository_install_dir, deactivate=True ) if installed_repository_dict and 'converter_path' in installed_repository_dict: - load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) + shed_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) if installed_repository_dict and 'display_path' in installed_repository_dict: - load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) + shed_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. @@ -496,7 +496,7 @@ tool_shed_repository.uninstalled = True # Remove all installed tool dependencies. for tool_dependency in tool_shed_repository.installed_tool_dependencies: - uninstalled, error_message = remove_tool_dependency( trans, tool_dependency ) + uninstalled, error_message = shed_util.remove_tool_dependency( trans, tool_dependency ) if error_message: errors = '%s %s' % ( errors, error_message ) tool_shed_repository.deleted = True @@ -553,7 +553,7 @@ items = tmp_url.split( 'repos' ) tool_shed_url = items[ 0 ] repo_path = items[ 1 ] - tool_shed_url = clean_tool_shed_url( tool_shed_url ) + tool_shed_url = shed_util.clean_tool_shed_url( tool_shed_url ) return suc.url_join( tool_shed_url, 'repos', repo_path, changeset_revision ) @web.json @web.require_admin @@ -570,7 +570,7 @@ name, owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which it was installed. """ - repository = get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) url = suc.url_join( tool_shed_url, 'repository/get_repository_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ @@ -585,7 +585,7 @@ text = '' return text def get_versions_of_tool( self, app, guid ): - tool_version = get_tool_version( app, guid ) + tool_version = shed_util.get_tool_version( app, guid ) return tool_version.get_version_ids( app, reverse=True ) @web.expose @web.require_admin @@ -614,10 +614,10 @@ tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', tool_shed_repository.repo_path( trans.app ) ) - installed_tool_dependencies = handle_tool_dependencies( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies ) + installed_tool_dependencies = shed_util.handle_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.model.ToolDependency.installation_status.ERROR: message += ' %s' % installed_tool_dependency.error_message @@ -644,7 +644,7 @@ tool_dependency_ids = util.listify( params.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) tool_dependencies.append( tool_dependency ) if kwd.get( 'install_tool_dependencies_button', False ): # Filter tool dependencies to only those that are installed. @@ -691,7 +691,7 @@ tool_shed_repository, repo_info_dict = tup repo_info_dict = tool_shed_decode( repo_info_dict ) # Clone each repository to the configured location. - update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING ) + shed_util.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING ) repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple relative_clone_dir = self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) @@ -702,10 +702,10 @@ if cloned_ok: if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. - current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) + current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) if current_ctx_rev != ctx_rev: repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) - pull_repository( repo, repository_clone_url, current_changeset_revision ) + shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) self.handle_repository_contents( trans, tool_shed_repository=tool_shed_repository, @@ -720,9 +720,9 @@ metadata = tool_shed_repository.metadata if 'tools' in metadata: # Get the tool_versions from the tool shed for each tool in the installed change set. - update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + shed_util.update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) url = suc.url_join( tool_shed_url, '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ @@ -732,7 +732,7 @@ response.close() if text: tool_version_dicts = from_json_string( text ) - handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository ) + shed_util.handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository ) else: message += "Version information for the tools included in the <b>%s</b> repository is missing. " % name message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions " @@ -741,20 +741,20 @@ if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: work_dir = tempfile.mkdtemp() # Install tool dependencies. - update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + shed_util.update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir )#relative_install_dir ) - installed_tool_dependencies = handle_tool_dependencies( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies ) + installed_tool_dependencies = shed_util.handle_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies ) try: shutil.rmtree( work_dir ) except: pass - update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) + shed_util.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. self.set_repository_attributes( trans, @@ -788,34 +788,34 @@ trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() if 'tool_dependencies' in metadata_dict and not reinstalling: - tool_dependencies = create_tool_dependency_objects( trans.app, tool_shed_repository, relative_install_dir, set_status=True ) + tool_dependencies = shed_util.create_tool_dependency_objects( trans.app, tool_shed_repository, relative_install_dir, set_status=True ) if 'tools' in metadata_dict: - tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) + tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = get_tool_index_sample_files( sample_files ) - copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) + tool_index_sample_files = shed_util.get_tool_index_sample_files( sample_files ) + shed_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = get_repository_tools_tups( trans.app, metadata_dict ) + repository_tools_tups = shed_util.get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = handle_missing_data_table_entry( trans.app, relative_install_dir, tool_path, repository_tools_tups ) + repository_tools_tups = shed_util.handle_missing_data_table_entry( trans.app, relative_install_dir, tool_path, repository_tools_tups ) # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups, sample_files_copied = handle_missing_index_file( trans.app, - tool_path, - sample_files, - repository_tools_tups, - sample_files_copied ) + repository_tools_tups, sample_files_copied = shed_util.handle_missing_index_file( trans.app, + tool_path, + sample_files, + repository_tools_tups, + sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - copy_sample_files( trans.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - add_to_tool_panel( app=trans.app, - repository_name=tool_shed_repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=tool_shed_repository.owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=True ) + shed_util.copy_sample_files( trans.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) + shed_util.add_to_tool_panel( app=trans.app, + repository_name=tool_shed_repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + repository_tools_tups=repository_tools_tups, + owner=tool_shed_repository.owner, + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=True ) if 'datatypes' in metadata_dict: tool_shed_repository.status = trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -827,16 +827,16 @@ files_dir = os.path.join( shed_config_dict['tool_path'], files_dir ) datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', files_dir ) # Load data types required by tools. - converter_path, display_path = alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, files_dir, override=False ) + converter_path, display_path = shed_util.alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, files_dir, override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. - repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, - name=tool_shed_repository.name, - owner=tool_shed_repository.owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) + repository_dict = shed_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, + name=tool_shed_repository.name, + owner=tool_shed_repository.owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters trans.app.datatypes_registry.load_datatype_converters( trans.app.toolbox, installed_repository_dict=repository_dict ) @@ -851,7 +851,7 @@ status = params.get( 'status', 'done' ) repository_id = kwd[ 'id' ] operation = kwd.get( 'operation', None ) - repository = get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans, repository_id ) if not repository: return trans.show_error_message( 'Invalid repository specified.' ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: @@ -866,7 +866,7 @@ ( repository.name, repository.owner, repository.installed_changeset_revision, ( 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 = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + shed_tool_conf, tool_path, relative_install_dir = shed_util.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, repository.name ) ) else: @@ -954,9 +954,9 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - tool_dependency_ids = get_tool_dependency_ids( as_string=False, **kwd ) + tool_dependency_ids = shed_util.get_tool_dependency_ids( as_string=False, **kwd ) # We need a tool_shed_repository, so get it from one of the tool_dependencies. - tool_dependency = get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) + tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) tool_shed_repository = tool_dependency.tool_shed_repository self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % tool_shed_repository.name self.tool_dependency_grid.global_actions = \ @@ -997,7 +997,7 @@ elif operation == 'uninstall': tool_dependencies_for_uninstallation = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) if tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLED, trans.model.ToolDependency.installation_status.ERROR ]: tool_dependencies_for_uninstallation.append( tool_dependency ) @@ -1012,7 +1012,7 @@ if trans.app.config.tool_dependency_dir: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, trans.model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) @@ -1156,17 +1156,17 @@ **new_kwd ) ) else: log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name ) - tool_shed_repository = create_or_update_tool_shed_repository( app=trans.app, - name=name, - description=description, - installed_changeset_revision=changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=trans.model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=changeset_revision, - owner=repository_owner, - dist_to_shed=False ) + tool_shed_repository = shed_util.create_or_update_tool_shed_repository( app=trans.app, + name=name, + description=description, + installed_changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=trans.model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=changeset_revision, + owner=repository_owner, + dist_to_shed=False ) created_or_updated_tool_shed_repositories.append( tool_shed_repository ) filtered_repo_info_dicts.append( tool_shed_encode( repo_info_dict ) ) if created_or_updated_tool_shed_repositories: @@ -1288,14 +1288,14 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] - tool_shed_repository = get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) no_changes = kwd.get( 'no_changes', '' ) no_changes_checked = CheckboxField.is_checked( no_changes ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section = kwd.get( 'tool_panel_section', '' ) - shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) - repository_clone_url = generate_clone_url_for_installed_repository( trans, tool_shed_repository ) + shed_tool_conf, tool_path, relative_install_dir = shed_util.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans, tool_shed_repository ) clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) @@ -1307,9 +1307,9 @@ if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if not tool_panel_dict: - tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) else: - tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) # Fix this to handle the case where the tools are distributed across in more than 1 ToolSection - this assumes everything was loaded into 1 # section (or no section) in the tool panel. tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] @@ -1353,18 +1353,18 @@ else: tool_section = None # The repository's status must be updated from 'Uninstall' to 'New' when initiating reinstall so the repository_installation_updater will function. - tool_shed_repository = create_or_update_tool_shed_repository( trans.app, - tool_shed_repository.name, - tool_shed_repository.description, - tool_shed_repository.installed_changeset_revision, - tool_shed_repository.ctx_rev, - repository_clone_url, - tool_shed_repository.metadata, - trans.model.ToolShedRepository.installation_status.NEW, - tool_shed_repository.installed_changeset_revision, - tool_shed_repository.owner, - tool_shed_repository.dist_to_shed ) - ctx_rev = get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) + tool_shed_repository = shed_util.create_or_update_tool_shed_repository( trans.app, + tool_shed_repository.name, + tool_shed_repository.description, + tool_shed_repository.installed_changeset_revision, + tool_shed_repository.ctx_rev, + repository_clone_url, + tool_shed_repository.metadata, + trans.model.ToolShedRepository.installation_status.NEW, + tool_shed_repository.installed_changeset_revision, + tool_shed_repository.owner, + tool_shed_repository.dist_to_shed ) + ctx_rev = shed_util.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) repo_info_dict = kwd.get( 'repo_info_dict', None ) # The repo_info_dict should be encoded. if not repo_info_dict: @@ -1450,11 +1450,11 @@ #clone_path, clone_directory = os.path.split( clone_dir ) changeset_revisions = util.listify( text ) for previous_changeset_revision in changeset_revisions: - tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, - tool_shed, - repository_name, - repository_owner, - previous_changeset_revision ) + tool_shed_repository = shed_util.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, + tool_shed, + repository_name, + repository_owner, + previous_changeset_revision ) if tool_shed_repository and tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]: return tool_shed_repository, previous_changeset_revision return None, None @@ -1462,11 +1462,11 @@ @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): repository_id = kwd[ 'id' ] - tool_shed_repository = get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) metadata = tool_shed_repository.metadata tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) - ctx_rev = get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) - repository_clone_url = generate_clone_url_for_installed_repository( trans, tool_shed_repository ) + ctx_rev = shed_util.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans, tool_shed_repository ) repository_dependencies = self.get_repository_dependencies( trans=trans, repository_id=repository_id, repository_name=tool_shed_repository.name, @@ -1486,7 +1486,7 @@ if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if tool_panel_dict: - if panel_entry_per_tool( tool_panel_dict ): + if shed_util.panel_entry_per_tool( tool_panel_dict ): # TODO: Fix this to handle the case where the tools are distributed across in more than 1 ToolSection. The # following assumes everything was loaded into 1 section (or no section) in the tool panel. tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] @@ -1570,9 +1570,9 @@ @web.require_admin def reset_repository_metadata( self, trans, id ): """Reset all metadata on a single installed tool shed repository.""" - repository = get_installed_tool_shed_repository( trans, id ) + repository = suc.get_installed_tool_shed_repository( trans, id ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) - repository_clone_url = generate_clone_url_for_installed_repository( trans, repository ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata @@ -1587,7 +1587,7 @@ persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: - update_in_shed_tool_config( trans.app, repository ) + suc.update_in_shed_tool_config( trans.app, repository ) trans.sa_session.add( repository ) trans.sa_session.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name @@ -1607,7 +1607,7 @@ @web.require_admin def reset_to_install( self, trans, **kwd ): """An error occurred while cloning the repository, so reset everything necessary to enable another attempt.""" - repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if kwd.get( 'reset_repository', False ): self.set_repository_attributes( trans, repository, @@ -1642,7 +1642,7 @@ @web.require_admin def set_tool_versions( self, trans, **kwd ): # Get the tool_versions from the tool shed for each tool in the installed change set. - repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) + repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) url = suc.url_join( tool_shed_url, 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ @@ -1652,7 +1652,7 @@ response.close() if text: tool_version_dicts = from_json_string( text ) - handle_tool_versions( trans.app, tool_version_dicts, repository ) + shed_util.handle_tool_versions( trans.app, tool_version_dicts, repository ) message = "Tool versions have been set for all included tools." status = 'done' else: @@ -1660,7 +1660,7 @@ message += "Reset all of this reppository's metadata in the tool shed, then set the installed tool versions " message ++ "from the installed repository's <b>Repository Actions</b> menu. " status = 'error' - shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + shed_tool_conf, tool_path, relative_install_dir = shed_util.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, @@ -1699,7 +1699,7 @@ tool_dependency_ids = util.listify( params.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) tool_dependencies.append( tool_dependency ) tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository if kwd.get( 'uninstall_tool_dependencies_button', False ): @@ -1710,7 +1710,7 @@ if tool_dependency.can_uninstall: tool_dependencies_for_uninstallation.append( tool_dependency ) for tool_dependency in tool_dependencies_for_uninstallation: - uninstalled, error_message = remove_tool_dependency( trans, tool_dependency ) + uninstalled, error_message = shed_util.remove_tool_dependency( trans, tool_dependency ) if error_message: errors = True message = '%s %s' % ( message, error_message ) @@ -1744,12 +1744,12 @@ changeset_revision = params.get( 'changeset_revision', None ) latest_changeset_revision = params.get( 'latest_changeset_revision', None ) latest_ctx_rev = params.get( 'latest_ctx_rev', None ) - repository = get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) + repository = shed_util.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) if changeset_revision and latest_changeset_revision and latest_ctx_rev: if changeset_revision == latest_changeset_revision: message = "The installed repository named '%s' is current, there are no updates available. " % name else: - shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + shed_tool_conf, tool_path, relative_install_dir = shed_util.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: if tool_path: repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) ) @@ -1757,9 +1757,9 @@ repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) repo = hg.repository( suc.get_configured_ui(), path=repo_files_dir ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) - pull_repository( repo, repository_clone_url, latest_ctx_rev ) + shed_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) suc.update_repository( repo, latest_ctx_rev ) - tool_shed = clean_tool_shed_url( tool_shed_url ) + tool_shed = shed_util.clean_tool_shed_url( tool_shed_url ) # Update the repository metadata. metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, @@ -1779,10 +1779,10 @@ trans.sa_session.flush() # Create tool_dependency records if necessary. if 'tool_dependencies' in metadata_dict: - tool_dependencies = create_tool_dependency_objects( trans.app, repository, relative_install_dir, set_status=False ) + tool_dependencies = shed_util.create_tool_dependency_objects( trans.app, repository, relative_install_dir, set_status=False ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % ( name, latest_changeset_revision ) # See if any tool dependencies can be installed. - shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + shed_tool_conf, tool_path, relative_install_dir = shed_util.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if repository.missing_tool_dependencies: message += "Click the name of one of the missing tool dependencies listed below to install tool dependencies." else: @@ -1802,7 +1802,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_installed_tool_shed_repository( trans, repository_id ) + repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repository_metadata = repository.metadata shed_config_dict = repository.get_shed_config_dict( trans.app ) tool_metadata = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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