galaxy-commits March 2014

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commit/galaxy-central: greg: Don't call the tool shed when loading the Galaxy tool panel at server startup.
by commits-noreply＠bitbucket.org 30 Mar '14

30 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8aabd0a1acf8/ Changeset: 8aabd0a1acf8 User: greg Date: 2014-03-30 23:42:22 Summary: Don't call the tool shed when loading the Galaxy tool panel at server startup. Affected #: 1 file diff -r ad89e3c86e4c765b24e145e7cdbdbf3ada7889fb -r 8aabd0a1acf8439553970fcbd5661f2ec8b34884 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -261,57 +261,67 @@ for index, integrated_panel_key in enumerate( self.integrated_tool_panel.keys() ): if key == integrated_panel_key: panel_dict.insert( index, key, tool ) - inserted = True + if not inserted: + inserted = True if not inserted: - if tool.guid is None or \ - tool.tool_shed is None or \ - tool.repository_name is None or \ - tool.repository_owner is None or \ - tool.installed_changeset_revision is None: - # We have a tool that was not installed from the Tool Shed, but is also not yet defined in - # integrated_tool_panel.xml, so append it to the tool panel. - panel_dict[ key ] = tool - log.debug( "Loaded tool id: %s, version: %s into tool panel.." % ( tool.id, tool.version ) ) - else: - # We are in the process of installing the tool. The version lineage chain will not yet be - # built on the Galaxy side, so we have to get it from the Tool Shed. - tool_shed_url = suc.get_url_from_tool_shed( self.app, str( tool.tool_shed ) ) - # get_versions_of_tool( self, trans, name, owner, changeset_revision, encoded_guid ) - params = '?name=%s&owner=%s&changeset_revision=%s&encoded_guid=%s' % \ - ( str( tool.repository_name ), - str( tool.repository_owner ), - str( tool.installed_changeset_revision ), - encoding_util.tool_shed_encode( tool.guid ) ) - url = suc.url_join( tool_shed_url, 'repository/get_versions_of_tool%s' % params ) - try: - # For backward compatibility - some versions of the Tool Shed will not have the - # get_versions_of_tool() method. - raw_text = common_util.tool_shed_get( self.app, tool_shed_url, url ) - tool_lineage_ids = json.loads( raw_text ) - except Exception, e: - log.exception( "Error with url\n%s\n%s" % ( str( url ), str( e ) ) ) - tool_lineage_ids = [] - for lineage_id in tool_lineage_ids: - if lineage_id in self.tools_by_id: - loaded_version_key = 'tool_%s' % lineage_id - if loaded_version_key in panel_dict: - if not already_loaded: - already_loaded = True - # Even though a version of the tool is loaded in the tool panel, we need to find out if it - # is the most recent version. - key = 'tool_%s' % tool.guid - index = panel_dict.keys().index( loaded_version_key ) - if loaded_version_key > key: + # Check the tool's installed versions. + for lineage_id in tool.tool_version_ids: + lineage_id_key = 'tool_%s' % lineage_id + for index, integrated_panel_key in enumerate( self.integrated_tool_panel.keys() ): + if lineage_id_key == integrated_panel_key: + panel_dict.insert( index, key, tool ) + if not inserted: + inserted = True + if not inserted: + if tool.guid is None or \ + tool.tool_shed is None or \ + tool.repository_name is None or \ + tool.repository_owner is None or \ + tool.installed_changeset_revision is None: + # We have a tool that was not installed from the Tool Shed, but is also not yet defined in + # integrated_tool_panel.xml, so append it to the tool panel. + panel_dict[ key ] = tool + log.debug( "Loaded tool id: %s, version: %s into tool panel.." % ( tool.id, tool.version ) ) + else: + # We are in the process of installing the tool. The version lineage chain will not yet be + # built on the Galaxy side, so we have to get it from the Tool Shed. + tool_shed_url = suc.get_url_from_tool_shed( self.app, str( tool.tool_shed ) ) + # get_versions_of_tool( self, trans, name, owner, changeset_revision, encoded_guid ) + params = '?name=%s&owner=%s&changeset_revision=%s&encoded_guid=%s' % \ + ( str( tool.repository_name ), + str( tool.repository_owner ), + str( tool.installed_changeset_revision ), + encoding_util.tool_shed_encode( tool.guid ) ) + url = suc.url_join( tool_shed_url, 'repository/get_versions_of_tool%s' % params ) + try: + # For backward compatibility - some versions of the Tool Shed will not have the + # get_versions_of_tool() method. + raw_text = common_util.tool_shed_get( self.app, tool_shed_url, url ) + tool_lineage_ids = json.loads( raw_text ) + except Exception, e: + log.exception( "Error with url\n%s\n%s" % ( str( url ), str( e ) ) ) + tool_lineage_ids = [] + for lineage_id in tool_lineage_ids: + if lineage_id in self.tools_by_id: + loaded_version_key = 'tool_%s' % lineage_id + if loaded_version_key in panel_dict: + if not already_loaded: + already_loaded = True + # Even though a version of the tool is loaded in the tool panel, we need to find out if it + # is the most recent version. + key = 'tool_%s' % tool.guid index = panel_dict.keys().index( loaded_version_key ) - del panel_dict[ loaded_version_key ] - panel_dict.insert( index, key, tool ) - log.debug( "Loaded tool id: %s, version: %s into tool panel..." % ( tool.id, tool.version ) ) - inserted = True - break - if not already_loaded: - # If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel. - panel_dict[ key ] = tool - log.debug( "Loaded tool id: %s, version: %s into tool panel...." % ( tool.id, tool.version ) ) + if loaded_version_key > key: + index = panel_dict.keys().index( loaded_version_key ) + del panel_dict[ loaded_version_key ] + panel_dict.insert( index, key, tool ) + log.debug( "Loaded tool id: %s, version: %s into tool panel..." % ( tool.id, tool.version ) ) + inserted = True + break + if not already_loaded: + # If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel. + panel_dict[ key ] = tool + log.debug( "Loaded tool id: %s, version: %s into tool panel...." % ( tool.id, tool.version ) ) def load_tool_panel( self ): for key, val in self.integrated_tool_panel.items(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Really fix broken tool shed functional test.
by commits-noreply＠bitbucket.org 30 Mar '14

30 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad89e3c86e4c/ Changeset: ad89e3c86e4c User: greg Date: 2014-03-30 22:35:44 Summary: Really fix broken tool shed functional test. Affected #: 1 file diff -r 3ae4eed1caf5a2efcc1e5721fb4fae8250220927 -r ad89e3c86e4c765b24e145e7cdbdbf3ada7889fb test/tool_shed/functional/test_1430_repair_installed_repository.py --- a/test/tool_shed/functional/test_1430_repair_installed_repository.py +++ b/test/tool_shed/functional/test_1430_repair_installed_repository.py @@ -144,7 +144,7 @@ This is step 2 - Uninstall the filter_1430 repository. ''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filter_1430', common.test_user_1_name ) - strings_displayed = [ 'Uninstalling this repository will affect the following dependent items' ] + strings_displayed = [ 'Uninstalling this repository will result in the following' ] strings_not_displayed = [] self.uninstall_repository( installed_repository, strings_displayed=strings_displayed, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix broken tool shed functional test.
by commits-noreply＠bitbucket.org 30 Mar '14

30 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3ae4eed1caf5/ Changeset: 3ae4eed1caf5 User: greg Date: 2014-03-30 22:33:56 Summary: Fix broken tool shed functional test. Affected #: 1 file diff -r f86fcd8dd3c350b6cfe3d0c5e0a809bab5e62469 -r 3ae4eed1caf5a2efcc1e5721fb4fae8250220927 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -313,6 +313,76 @@ .outerjoin( model.Category.table ) +class CertifiedLevelOneRepositoryGrid( RepositoryGrid ): + columns = [ c for c in RepositoryGrid.columns ] + + def build_initial_query( self, trans, **kwd ): + clause_list = [] + for repository in trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ): + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + # Get the list of latest installable changeset revision for each repository since that is all + # that is currently configured for testing. + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION ]: + # We can use the changelog tip. + latest_changeset_revision = str( repo.changectx( repo.changelog.tip() ) ) + else: + latest_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) + if latest_changeset_revision not in [ None, suc.INITIAL_CHANGELOG_HASH ]: + encoded_repository_id = trans.security.encode_id( repository.id ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + encoded_repository_id, + latest_changeset_revision ) + # Filter out repository revisions that have not been tested. + if repository_metadata.time_last_tested is not None and repository_metadata.tool_test_results is not None: + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION ]: + # Look in the tool_test_results dictionary for installation errors. + try: + tool_test_results_dict = repository_metadata.tool_test_results[ -1 ] + except Exception, e: + # The repository is not certified. + continue + if 'installation_errors' in tool_test_results_dict: + continue + # The revision is level 1 certified + clause_list.append( "%s=%d and %s='%s'" % ( model.RepositoryMetadata.table.c.repository_id, + repository.id, + model.RepositoryMetadata.table.c.changeset_revision, + changeset_revision ) ) + else: + # We have an unrestricted repository. + if latest_changeset_revision.includes_tools: + if latest_changeset_revision.tools_functionally_correct: + # The revision is level 1 certified + clause_list.append( "%s=%d and %s='%s'" % ( model.RepositoryMetadata.table.c.repository_id, + repository.id, + model.RepositoryMetadata.table.c.changeset_revision, + changeset_revision ) ) + else: + # Look in the tool_test_results dictionary for installation errors. + try: + tool_test_results_dict = repository_metadata.tool_test_results[ -1 ] + except Exception, e: + # The repository is not certified. + continue + if 'installation_errors' in tool_test_results_dict: + continue + # The revision is level 1 certified + clause_list.append( "%s=%d and %s='%s'" % ( model.RepositoryMetadata.table.c.repository_id, + repository.id, + model.RepositoryMetadata.table.c.changeset_revision, + changeset_revision ) ) + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.RepositoryMetadata.table ) \ + .filter( or_( *clause_list ) ) \ + .join( model.User.table ) \ + .outerjoin( model.RepositoryCategoryAssociation.table ) \ + .outerjoin( model.Category.table ) + + class EmailAlertsRepositoryGrid( RepositoryGrid ): columns = [ RepositoryGrid.NameColumn( "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: greg: Fix for installing a repository into Galaxy that contains a tool to be loaded into the tool panel where another version in the tool's lineage chain is already loaded into the tool panel. An additional entry will no longer be made. Instead, a single entry will exist for the entire lineage chain.
by commits-noreply＠bitbucket.org 30 Mar '14

30 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f86fcd8dd3c3/ Changeset: f86fcd8dd3c3 User: greg Date: 2014-03-30 22:25:25 Summary: Fix for installing a repository into Galaxy that contains a tool to be loaded into the tool panel where another version in the tool's lineage chain is already loaded into the tool panel. An additional entry will no longer be made. Instead, a single entry will exist for the entire lineage chain. Affected #: 5 files diff -r f83f4d9965283e8dc8640698262da52080081496 -r f86fcd8dd3c350b6cfe3d0c5e0a809bab5e62469 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -63,7 +63,9 @@ from galaxy.web.form_builder import SelectField from galaxy.model.item_attrs import Dictifiable from galaxy.model import Workflow -from tool_shed.util import shed_util_common +from tool_shed.util import common_util +from tool_shed.util import encoding_util +from tool_shed.util import shed_util_common as suc from .loader import load_tool, template_macro_params from .wrappers import ( ToolParameterValueWrapper, @@ -227,9 +229,10 @@ return shed_config_dict return default - def __add_tool_to_tool_panel( self, tool_id, panel_component, section=False ): + def __add_tool_to_tool_panel( self, tool, panel_component, section=False ): # See if a version of this tool is already loaded into the tool panel. The value of panel_component # will be a ToolSection (if the value of section=True) or self.tool_panel (if section=False). + tool_id = str( tool.id ) tool = self.tools_by_id[ tool_id ] if section: panel_dict = panel_component.elems @@ -244,7 +247,14 @@ if loaded_version_key in panel_dict: already_loaded = True break - if not already_loaded: + if already_loaded: + if tool.lineage_ids.index( tool_id ) > tool.lineage_ids.index( lineage_id ): + key = 'tool_%s' % tool.id + index = panel_dict.keys().index( loaded_version_key ) + del panel_dict[ loaded_version_key ] + panel_dict.insert( index, key, tool ) + log.debug( "Loaded tool id: %s, version: %s into tool panel." % ( tool.id, tool.version ) ) + else: inserted = False key = 'tool_%s' % tool.id # The value of panel_component is the in-memory tool panel dictionary. @@ -253,22 +263,62 @@ panel_dict.insert( index, key, tool ) inserted = True if not inserted: - # If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel. - panel_dict[ key ] = tool - log.debug( "Loaded tool id: %s, version: %s into tool panel." % ( tool.id, tool.version ) ) - elif tool.lineage_ids.index( tool_id ) > tool.lineage_ids.index( lineage_id ): - key = 'tool_%s' % tool.id - index = panel_dict.keys().index( loaded_version_key ) - del panel_dict[ loaded_version_key ] - panel_dict.insert( index, key, tool ) - log.debug( "Loaded tool id: %s, version: %s into tool panel." % ( tool.id, tool.version ) ) + if tool.guid is None or \ + tool.tool_shed is None or \ + tool.repository_name is None or \ + tool.repository_owner is None or \ + tool.installed_changeset_revision is None: + # We have a tool that was not installed from the Tool Shed, but is also not yet defined in + # integrated_tool_panel.xml, so append it to the tool panel. + panel_dict[ key ] = tool + log.debug( "Loaded tool id: %s, version: %s into tool panel.." % ( tool.id, tool.version ) ) + else: + # We are in the process of installing the tool. The version lineage chain will not yet be + # built on the Galaxy side, so we have to get it from the Tool Shed. + tool_shed_url = suc.get_url_from_tool_shed( self.app, str( tool.tool_shed ) ) + # get_versions_of_tool( self, trans, name, owner, changeset_revision, encoded_guid ) + params = '?name=%s&owner=%s&changeset_revision=%s&encoded_guid=%s' % \ + ( str( tool.repository_name ), + str( tool.repository_owner ), + str( tool.installed_changeset_revision ), + encoding_util.tool_shed_encode( tool.guid ) ) + url = suc.url_join( tool_shed_url, 'repository/get_versions_of_tool%s' % params ) + try: + # For backward compatibility - some versions of the Tool Shed will not have the + # get_versions_of_tool() method. + raw_text = common_util.tool_shed_get( self.app, tool_shed_url, url ) + tool_lineage_ids = json.loads( raw_text ) + except Exception, e: + log.exception( "Error with url\n%s\n%s" % ( str( url ), str( e ) ) ) + tool_lineage_ids = [] + for lineage_id in tool_lineage_ids: + if lineage_id in self.tools_by_id: + loaded_version_key = 'tool_%s' % lineage_id + if loaded_version_key in panel_dict: + if not already_loaded: + already_loaded = True + # Even though a version of the tool is loaded in the tool panel, we need to find out if it + # is the most recent version. + key = 'tool_%s' % tool.guid + index = panel_dict.keys().index( loaded_version_key ) + if loaded_version_key > key: + index = panel_dict.keys().index( loaded_version_key ) + del panel_dict[ loaded_version_key ] + panel_dict.insert( index, key, tool ) + log.debug( "Loaded tool id: %s, version: %s into tool panel..." % ( tool.id, tool.version ) ) + inserted = True + break + if not already_loaded: + # If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel. + panel_dict[ key ] = tool + log.debug( "Loaded tool id: %s, version: %s into tool panel...." % ( tool.id, tool.version ) ) def load_tool_panel( self ): for key, val in self.integrated_tool_panel.items(): if isinstance( val, Tool ): tool_id = key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: - self.__add_tool_to_tool_panel( tool_id, self.tool_panel, section=False ) + self.__add_tool_to_tool_panel( val, self.tool_panel, section=False ) elif isinstance( val, Workflow ): workflow_id = key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: @@ -288,7 +338,7 @@ if isinstance( section_val, Tool ): tool_id = section_key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: - self.__add_tool_to_tool_panel( tool_id, section, section=True ) + self.__add_tool_to_tool_panel( section_val, section, section=True ) elif isinstance( section_val, Workflow ): workflow_id = section_key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: @@ -431,8 +481,8 @@ def __get_tool_version( self, tool_id ): """Return a ToolVersion if one exists for the tool_id""" return self.app.install_model.context.query( self.app.install_model.ToolVersion ) \ - .filter( self.app.install_model.ToolVersion.table.c.tool_id == tool_id ) \ - .first() + .filter( self.app.install_model.ToolVersion.table.c.tool_id == tool_id ) \ + .first() def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ): return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ @@ -546,14 +596,15 @@ tta = self.app.model.ToolTagAssociation( tool_id=tool.id, tag_id=tag.id ) self.sa_session.add( tta ) self.sa_session.flush() - #if tool.id not in self.tools_by_id: - # Allow for the same tool to be loaded into multiple places in the tool panel. We have to handle the case where the tool is contained - # in a repository installed from the tool shed, and the Galaxy administrator has retrieved updates to the installed repository. In this - # case, the tool may have been updated, but the version was not changed, so the tool should always be reloaded here. We used to only load - # the tool if it's it was not found in self.tools_by_id, but performing that check did not enable this scenario. + # Allow for the same tool to be loaded into multiple places in the tool panel. We have to handle + # the case where the tool is contained in a repository installed from the tool shed, and the Galaxy + # administrator has retrieved updates to the installed repository. In this case, the tool may have + # been updated, but the version was not changed, so the tool should always be reloaded here. We used + # to only load the tool if it's it was not found in self.tools_by_id, but performing that check did + # not enable this scenario. self.tools_by_id[ tool.id ] = tool if load_panel_dict: - self.__add_tool_to_tool_panel( tool.id, panel_dict, section=isinstance( panel_dict, ToolSection ) ) + self.__add_tool_to_tool_panel( tool, panel_dict, section=isinstance( panel_dict, ToolSection ) ) # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file. if key in integrated_panel_dict or index is None: integrated_panel_dict[ key ] = tool @@ -1020,8 +1071,8 @@ def tool_version( self ): """Return a ToolVersion if one exists for our id""" return self.app.install_model.context.query( self.app.install_model.ToolVersion ) \ - .filter( self.app.install_model.ToolVersion.table.c.tool_id == self.id ) \ - .first() + .filter( self.app.install_model.ToolVersion.table.c.tool_id == self.id ) \ + .first() @property def tool_versions( self ): @@ -1043,11 +1094,11 @@ def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. if self.tool_shed: - return shed_util_common.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 suc.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_tool_configuration(self, job_params=None): @@ -1359,7 +1410,7 @@ lock = threading.Lock() lock.acquire( True ) try: - self.help.text = shed_util_common.set_image_paths( self.app, self.repository_id, self.help.text ) + self.help.text = suc.set_image_paths( self.app, self.repository_id, self.help.text ) except Exception, e: log.exception( "Exception in parse_help, so images may not be properly displayed:\n%s" % str( e ) ) finally: diff -r f83f4d9965283e8dc8640698262da52080081496 -r f86fcd8dd3c350b6cfe3d0c5e0a809bab5e62469 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 @@ -405,10 +405,6 @@ repo_information_dict = json.from_json_string( raw_text ) return repo_information_dict - def get_versions_of_tool( self, app, guid ): - tool_version = tool_util.get_tool_version( app, guid ) - return tool_version.get_version_ids( app, reverse=True ) - @web.expose @web.require_admin def import_workflow( self, trans, workflow_name, repository_id, **kwd ): @@ -1973,7 +1969,8 @@ tool_config = os.path.join( shed_config_dict.get( 'tool_path' ), tool_config ) tool = trans.app.toolbox.load_tool( os.path.abspath( tool_config ), guid=tool_metadata[ 'guid' ] ) if tool: - tool_lineage = self.get_versions_of_tool( trans.app, tool.id ) + tool_version = tool_util.get_tool_version( trans.app, str( tool.id ) ) + tool_lineage = tool_version.get_version_ids( trans.app, reverse=True ) break return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako", repository=repository, diff -r f83f4d9965283e8dc8640698262da52080081496 -r f86fcd8dd3c350b6cfe3d0c5e0a809bab5e62469 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -89,12 +89,13 @@ def browse_categories( self, trans, **kwd ): # The request came from the tool shed. if 'f-free-text-search' in kwd: - # Trick to enable searching repository name, description from the CategoryGrid. What we've done is rendered the search box for the - # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. Since we - # are searching repositories and not categories, redirect to browse_repositories(). + # Trick to enable searching repository name, description from the CategoryGrid. + # What we've done is rendered the search box for the RepositoryGrid on the grid.mako + # template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. + # Since we are searching repositories and not categories, redirect to browse_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: - # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository - # id to pass on. + # The value of 'id' has been set to the search string, which is a repository name. + # We'll try to get the desired encoded repository id to pass on. try: repository_name = kwd[ 'id' ] repository = suc.get_repository_by_name( trans.app, repository_name ) @@ -1906,41 +1907,35 @@ readme_files_dict=readme_files_dict, repo_info_dict=repo_info_dict ) - def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): + @web.json + def get_versions_of_tool( self, trans, name, owner, changeset_revision, encoded_guid ): + #def get_versions_of_tool( self, trans, repository_id, repository_metadata, guid ): """ - Return the tool lineage in descendant order for the received guid contained in the received - repsitory_metadata.tool_versions. + Return the tool version lineage chain in descending order for the received guid contained + in the repsitory_metadata.tool_versions column associated with the received changeset_revision + whose associated repository is associated with the received name and owner. """ - encoded_id = trans.security.encode_id( repository.id ) - repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) - # Initialize the tool lineage - tool_guid_lineage = [ guid ] - # Get all ancestor guids of the received guid. - current_child_guid = guid - for changeset in suc.reversed_upper_bounded_changelog( repo, repository_metadata.changeset_revision ): - ctx = repo.changectx( changeset ) - rm = suc.get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) ) - if rm: - parent_guid = rm.tool_versions.get( current_child_guid, None ) - if parent_guid: - tool_guid_lineage.append( parent_guid ) - current_child_guid = parent_guid - # Get all descendant guids of the received guid. - current_parent_guid = guid - for changeset in suc.reversed_lower_upper_bounded_changelog( repo, - repository_metadata.changeset_revision, - repository.tip( trans.app ) ): - ctx = repo.changectx( changeset ) - rm = suc.get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) ) - if rm: - tool_versions = rm.tool_versions - for child_guid, parent_guid in tool_versions.items(): - if parent_guid == current_parent_guid: - tool_guid_lineage.insert( 0, child_guid ) - current_parent_guid = child_guid - break - return tool_guid_lineage + guid = encoding_util.tool_shed_decode( encoded_guid ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + version_lineage = [] + if repository: + repository_id = trans.security.encode_id( repository.id ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + repository_id, + changeset_revision ) + if not repository_metadata: + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + updated_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, + repo, + changeset_revision ) + if updated_changeset_revision: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + repository_id, + updated_changeset_revision ) + if repository_metadata: + version_lineage = tool_util.get_version_lineage_for_tool( trans, repository_id, repository_metadata, guid ) + return version_lineage @web.expose def help( self, trans, **kwd ): @@ -3284,29 +3279,35 @@ guid = tool_metadata_dict[ 'guid' ] full_path_to_tool_config = os.path.abspath( relative_path_to_tool_config ) full_path_to_dir, tool_config_filename = os.path.split( full_path_to_tool_config ) - can_use_disk_file = tool_util.can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision ) + can_use_disk_file = tool_util.can_use_tool_config_disk_file( trans, + repository, + repo, + full_path_to_tool_config, + changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir - tool, valid, message, sample_files = tool_util.handle_sample_files_and_load_tool_from_disk( trans, - repo_files_dir, - repository_id, - full_path_to_tool_config, - work_dir ) + tool, valid, message, sample_files = \ + tool_util.handle_sample_files_and_load_tool_from_disk( trans, + repo_files_dir, + repository_id, + full_path_to_tool_config, + work_dir ) if message: status = 'error' else: - tool, message, sample_files = tool_util.handle_sample_files_and_load_tool_from_tmp_config( trans, - repo, - repository_id, - changeset_revision, - tool_config_filename, - work_dir ) + tool, message, sample_files = \ + tool_util.handle_sample_files_and_load_tool_from_tmp_config( trans, + repo, + repository_id, + changeset_revision, + tool_config_filename, + work_dir ) if message: status = 'error' suc.remove_dir( work_dir ) break if guid: - tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) + tool_lineage = tool_util.get_version_lineage_for_tool( trans, repository_id, repository_metadata, guid ) else: repository_metadata_id = None metadata = None diff -r f83f4d9965283e8dc8640698262da52080081496 -r f86fcd8dd3c350b6cfe3d0c5e0a809bab5e62469 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1180,9 +1180,9 @@ def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database.""" - # Make sure there are no duplicate records, and return the single unique record for the changeset_revision. Duplicate records were somehow - # created in the past. The cause of this issue has been resolved, but we'll leave this method as is for a while longer to ensure all duplicate - # records are removed. + # Make sure there are no duplicate records, and return the single unique record for the changeset_revision. + # Duplicate records were somehow created in the past. The cause of this issue has been resolved, but we'll + # leave this method as is for a while longer to ensure all duplicate records are removed. all_metadata_records = trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ diff -r f83f4d9965283e8dc8640698262da52080081496 -r f86fcd8dd3c350b6cfe3d0c5e0a809bab5e62469 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -524,6 +524,42 @@ app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id ) ) \ .first() +def get_version_lineage_for_tool( trans, repository_id, repository_metadata, guid ): + """ + Return the tool version lineage chain in descendant order for the received guid contained in the received + repsitory_metadata.tool_versions. + """ + repository = suc.get_repository_by_id( trans, repository_id ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + # Initialize the tool lineage + version_lineage = [ guid ] + # Get all ancestor guids of the received guid. + current_child_guid = guid + for changeset in suc.reversed_upper_bounded_changelog( repo, repository_metadata.changeset_revision ): + ctx = repo.changectx( changeset ) + rm = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, str( ctx ) ) + if rm: + parent_guid = rm.tool_versions.get( current_child_guid, None ) + if parent_guid: + version_lineage.append( parent_guid ) + current_child_guid = parent_guid + # Get all descendant guids of the received guid. + current_parent_guid = guid + for changeset in suc.reversed_lower_upper_bounded_changelog( repo, + repository_metadata.changeset_revision, + repository.tip( trans.app ) ): + ctx = repo.changectx( changeset ) + rm = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, str( ctx ) ) + if rm: + tool_versions = rm.tool_versions + for child_guid, parent_guid in tool_versions.items(): + if parent_guid == current_parent_guid: + version_lineage.insert( 0, child_guid ) + current_parent_guid = child_guid + break + return version_lineage + def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ): """ Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Add unit test for extra primary dataset collection.
by commits-noreply＠bitbucket.org 28 Mar '14

28 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f83f4d996528/ Changeset: f83f4d996528 User: jmchilton Date: 2014-03-29 00:33:03 Summary: Add unit test for extra primary dataset collection. Tests overridding various output properties (ext, dbkey, name, visible) with file name and galaxy.json, collecting from new_file_path versus job_working_directory, setting job output associations, and logic related to adding outputs to copied histories. Affected #: 1 file diff -r db607526191533fcc4bc60509e3c415ffdfd241d -r f83f4d9965283e8dc8640698262da52080081496 test/unit/tools/test_collect_primary_datasets.py --- /dev/null +++ b/test/unit/tools/test_collect_primary_datasets.py @@ -0,0 +1,186 @@ +import os +import json +import unittest + +import tools_support + +from galaxy import model + +DEFAULT_TOOL_OUTPUT = "out1" +DEFAULT_EXTRA_NAME = "test1" + + +class CollectPrimaryDatasetsTestCase( unittest.TestCase, tools_support.UsesApp, tools_support.UsesTools ): + + def setUp( self ): + self.setup_app( mock_model=False ) + object_store = MockObjectStore() + self.app.object_store = object_store + self._init_tool( tools_support.SIMPLE_TOOL_CONTENTS ) + self._setup_test_output( ) + self.app.config.collect_outputs_from = "job_working_directory" + + self.app.model.Dataset.object_store = object_store + + def tearDown( self ): + if self.app.model.Dataset.object_store is self.app.object_store: + self.app.model.Dataset.object_store = None + + def test_empty_collect( self ): + assert len( self._collect() ) == 0 + + def test_collect_multiple( self ): + path1 = self._setup_extra_file( name="test1" ) + path2 = self._setup_extra_file( name="test2" ) + + datasets = self._collect() + assert DEFAULT_TOOL_OUTPUT in datasets + self.assertEquals( len( datasets[ DEFAULT_TOOL_OUTPUT ] ), 2 ) + + created_hda_1 = datasets[ DEFAULT_TOOL_OUTPUT ][ "test1" ] + self.app.object_store.assert_created_with_path( created_hda_1.dataset, path1 ) + + created_hda_2 = datasets[ DEFAULT_TOOL_OUTPUT ][ "test2" ] + self.app.object_store.assert_created_with_path( created_hda_2.dataset, path2 ) + + # Test default metadata stuff + assert created_hda_1.visible + assert created_hda_1.dbkey == "?" + + def test_collect_hidden( self ): + self._setup_extra_file( visible="hidden" ) + created_hda = self._collect_default_extra() + assert not created_hda.visible + + def test_collect_ext( self ): + self._setup_extra_file( ext="txt" ) + created_hda = self._collect_default_extra() + assert created_hda.ext == "txt" + + def test_copied_to_imported_histories( self ): + self._setup_extra_file( ) + cloned_hda = self.hda.copy() + history_2 = self._new_history( hdas=[ cloned_hda ]) + assert len( history_2.datasets ) == 1 + + self._collect() + + # Make sure extra primary was copied to cloned history with + # cloned output. + assert len( history_2.datasets ) == 2 + + def test_dbkey_from_filename( self ): + self._setup_extra_file( dbkey="hg19" ) + created_hda = self._collect_default_extra() + assert created_hda.dbkey == "hg19" + + def test_dbkey_from_galaxy_json( self ): + path = self._setup_extra_file( ) + self._append_job_json( dict( dbkey="hg19" ), output_path=path ) + created_hda = self._collect_default_extra() + assert created_hda.dbkey == "hg19" + + def test_name_from_galaxy_json( self ): + path = self._setup_extra_file( ) + self._append_job_json( dict( name="test_from_json" ), output_path=path ) + created_hda = self._collect_default_extra() + assert "test_from_json" in created_hda.name + + def test_info_from_galaxy_json( self ): + path = self._setup_extra_file( ) + self._append_job_json( dict( info="extra output info" ), output_path=path ) + created_hda = self._collect_default_extra() + assert created_hda.info == "extra output info" + + def test_extension_from_galaxy_json( self ): + path = self._setup_extra_file( ) + self._append_job_json( dict( ext="txt" ), output_path=path ) + created_hda = self._collect_default_extra() + assert created_hda.ext == "txt" + + def test_new_file_path_collection( self ): + self.app.config.collect_outputs_from = "new_file_path" + self.app.config.new_file_path = self.test_directory + + self._setup_extra_file( ) + created_hda = self._collect_default_extra( job_working_directory="/tmp" ) + assert created_hda + + def test_job_param( self ): + self._setup_extra_file( ) + assert len( self.job.output_datasets ) == 1 + self._collect_default_extra() + assert len( self.job.output_datasets ) == 2 + extra_job_assoc = filter( lambda job_assoc: job_assoc.name.startswith( "__" ), self.job.output_datasets )[ 0 ] + assert extra_job_assoc.name == "__new_primary_file_out1|test1__" + + def _collect_default_extra( self, **kwargs ): + return self._collect( **kwargs )[ DEFAULT_TOOL_OUTPUT ][ DEFAULT_EXTRA_NAME ] + + def _collect( self, job_working_directory=None ): + if not job_working_directory: + job_working_directory = self.test_directory + return self.tool.collect_primary_datasets( self.outputs, job_working_directory ) + + def _append_job_json( self, object, output_path=None, line_type="new_primary_dataset" ): + object[ "type" ] = line_type + if output_path: + name = os.path.basename( output_path ) + object[ "filename" ] = name + line = json.dumps( object ) + with open( os.path.join( self.test_directory, "galaxy.json" ), "a" ) as f: + f.write( "%s\n" % line ) + + def _setup_extra_file( self, **kwargs ): + path = kwargs.get( "path", None ) + if not path: + name = kwargs.get( "name", DEFAULT_EXTRA_NAME ) + visible = kwargs.get( "visible", "visible" ) + ext = kwargs.get( "ext", "data" ) + template_args = ( self.hda.id, name, visible, ext ) + directory = kwargs.get( "directory", self.test_directory ) + path = os.path.join( directory, "primary_%s_%s_%s_%s" % template_args ) + if "dbkey" in kwargs: + path = "%s_%s" % ( path, kwargs[ "dbkey" ] ) + contents = kwargs.get( "contents", "test contents" ) + open( path, "w" ).write( contents ) + return path + + def _setup_test_output( self ): + dataset = model.Dataset() + dataset.external_filename = "example_output" # This way object store isn't asked about size... + self.hda = model.HistoryDatasetAssociation( name="test", dataset=dataset ) + job = model.Job() + job.add_output_dataset( DEFAULT_TOOL_OUTPUT, self.hda ) + self.app.model.context.add( job ) + self.job = job + self.history = self._new_history( hdas=[ self.hda ] ) + self.outputs = { DEFAULT_TOOL_OUTPUT: self.hda } + + def _new_history( self, hdas=[], flush=True ): + history = model.History() + self.app.model.context.add( history ) + for hda in hdas: + history.add_dataset( hda, set_hid=False ) + self.app.model.context.flush( ) + return history + + +class MockObjectStore( object ): + + def __init__( self ): + self.created_datasets = {} + + def update_from_file( self, dataset, file_name, create ): + if create: + self.created_datasets[ dataset ] = file_name + + def size( self, dataset ): + path = self.created_datasets[ dataset ] + return os.stat( path ).st_size + + def get_filename( self, dataset ): + return self.created_datasets[ dataset ] + + def assert_created_with_path( self, dataset, file_name ): + assert self.created_datasets[ dataset ] == file_name Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Bugfix: Problem with primary dataset collection on cloned histories.
by commits-noreply＠bitbucket.org 28 Mar '14

28 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db6075261915/ Changeset: db6075261915 User: jmchilton Date: 2014-03-28 23:49:50 Summary: Bugfix: Problem with primary dataset collection on cloned histories. Affected #: 1 file diff -r 35105e993ae91da02eb222db3007541bd4de4c3e -r db607526191533fcc4bc60509e3c415ffdfd241d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2841,7 +2841,7 @@ if outdata == dataset: continue new_data = primary_data.copy() - dataset.history.add( new_data ) + dataset.history.add_dataset( new_data ) self.sa_session.add( new_data ) self.sa_session.flush() return primary_datasets 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 commits-noreply＠bitbucket.org 28 Mar '14

28 Mar '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8a8ae4ca2480/ Changeset: 8a8ae4ca2480 User: natefoo Date: 2014-02-27 22:37:48 Summary: Rename ucsc_build_sites.txt to .sample. Affected #: 4 files diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 .hgignore --- a/.hgignore +++ b/.hgignore @@ -77,6 +77,7 @@ tool-data/shared/ucsc/builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt tool-data/*.loc tool-data/genome/* diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 run.sh --- a/run.sh +++ b/run.sh @@ -24,6 +24,7 @@ tool-data/shared/ensembl/builds.txt.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/ucsc/ucsc_build_sites.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/*.sample diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 tool-data/shared/ucsc/ucsc_build_sites.txt --- a/tool-data/shared/ucsc/ucsc_build_sites.txt +++ /dev/null @@ -1,7 +0,0 @@ -#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn -main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 -#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn -archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 -#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn -test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 -ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 tool-data/shared/ucsc/ucsc_build_sites.txt.sample --- /dev/null +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt.sample @@ -0,0 +1,7 @@ +#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn +main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 +#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn +archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 +#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn +test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 +ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 https://bitbucket.org/galaxy/galaxy-central/commits/35105e993ae9/ Changeset: 35105e993ae9 User: natefoo Date: 2014-03-28 21:44:54 Summary: Merged in natefoo/galaxy-central (pull request #340) Rename ucsc_build_sites.txt to .sample. Affected #: 4 files diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e .hgignore --- a/.hgignore +++ b/.hgignore @@ -77,6 +77,7 @@ tool-data/shared/ucsc/builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt tool-data/*.loc tool-data/genome/* diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e run.sh --- a/run.sh +++ b/run.sh @@ -24,6 +24,7 @@ tool-data/shared/ensembl/builds.txt.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/ucsc/ucsc_build_sites.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/*.sample diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e tool-data/shared/ucsc/ucsc_build_sites.txt --- a/tool-data/shared/ucsc/ucsc_build_sites.txt +++ /dev/null @@ -1,7 +0,0 @@ -#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn -main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 -#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn -archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 -#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn -test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 -ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e tool-data/shared/ucsc/ucsc_build_sites.txt.sample --- /dev/null +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt.sample @@ -0,0 +1,7 @@ +#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn +main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 +#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn +archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 +#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn +test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 +ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Disable manage_dependency_relationships by default to improve startup time.
by commits-noreply＠bitbucket.org 28 Mar '14

28 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e78c9aa7dc46/ Changeset: e78c9aa7dc46 User: natefoo Date: 2014-03-28 21:36:47 Summary: Disable manage_dependency_relationships by default to improve startup time. Affected #: 2 files diff -r 7815c237d0ddd998e300f6aec94b7a118e60420e -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -95,7 +95,7 @@ self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) - self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) ) + self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) try: diff -r 7815c237d0ddd998e300f6aec94b7a118e60420e -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -158,7 +158,7 @@ # Enable use of an in-memory registry with bi-directional relationships # between repositories (i.e., in addition to lists of dependencies for a # repository, keep an in-memory registry of dependent items for each repository. -#manage_dependency_relationships = True +#manage_dependency_relationships = False # XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator. 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 some missing semi-colons to javascript on templates/user/register.mako
by commits-noreply＠bitbucket.org 28 Mar '14

28 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7815c237d0dd/ Changeset: 7815c237d0dd User: dan Date: 2014-03-28 20:53:19 Summary: Add some missing semi-colons to javascript on templates/user/register.mako Affected #: 1 file diff -r 8af219b52f5ed11cccac4d49cb35ce71441cb91b -r 7815c237d0ddd998e300f6aec94b7a118e60420e templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -56,7 +56,7 @@ $(".errormessage").html(message) } else { var div = document.createElement("div"); - div.className = "errormessage" + div.className = "errormessage"; div.innerHTML = message; document.body.insertBefore(div, document.body.firstChild); } @@ -78,7 +78,7 @@ var validForm = true; var email = $('#email_input').val(); - var name = $('#name_input').val() + var name = $('#name_input').val(); if (email.length > 255){ renderError(error_text_email_long); validForm = false;} else if (!validateString(email,"email")){ renderError(error_text_email); validForm = false;} else if (!($('#password_input').val() === $('#password_check_input').val())){ renderError(error_text_password_match); validForm = false;} 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: Use encoded HDA ID in dataset/errors.mako
by commits-noreply＠bitbucket.org 28 Mar '14

28 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8af219b52f5e/ Changeset: 8af219b52f5e User: dan Date: 2014-03-28 20:52:08 Summary: Use encoded HDA ID in dataset/errors.mako Affected #: 2 files diff -r b1110a8e67c3b93da294eb3068d04b9249d914a9 -r 8af219b52f5ed11cccac4d49cb35ce71441cb91b lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -53,10 +53,12 @@ # Get the dataset sa_session = app.model.context if not isinstance( hda, model.HistoryDatasetAssociation ): + hda_id = hda try: - hda = sa_session.query( model.HistoryDatasetAssociation ).get( hda ) + hda = sa_session.query( model.HistoryDatasetAssociation ).get( hda_id ) + assert hda is not None, ValueError( "No HDA yet" ) except: - hda = sa_session.query( model.HistoryDatasetAssociation ).get( app.security.decode_id( hda ) ) + hda = sa_session.query( model.HistoryDatasetAssociation ).get( app.security.decode_id( hda_id ) ) assert isinstance( hda, model.HistoryDatasetAssociation ), ValueError( "Bad value provided for HDA (%s)." % ( hda ) ) self.hda = hda # Get the associated job diff -r b1110a8e67c3b93da294eb3068d04b9249d914a9 -r 8af219b52f5ed11cccac4d49cb35ce71441cb91b templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -61,7 +61,7 @@ <div class="toolFormTitle">Error Report</div><div class="toolFormBody"><form name="report_error" action="${h.url_for(controller='dataset', action='report_error')}" method="post" > - <input type="hidden" name="id" value="${hda.id}" /> + <input type="hidden" name="id" value="${trans.security.encode_id( hda.id)}" /><div class="form-row"><label>Your email</label><input type="text" name="email" size="40" value="${user_email}" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits March 2014