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/
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