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Source code for galaxy.tool_shed.galaxy_install.tools.data_manager

import errno
import logging
import os
import time

from galaxy.util import (
from galaxy.util.renamed_temporary_file import RenamedTemporaryFile
from galaxy.util.tool_shed.xml_util import parse_xml
from . import tool_panel_manager

log = logging.getLogger(__name__)

SHED_DATA_MANAGER_CONF_XML = """<?xml version="1.0"?>

[docs]class DataManagerHandler:
[docs] def __init__(self, app): self.app = app
@property def data_managers_path(self): tree, error_message = parse_xml(self.app.config.shed_data_manager_config_file) if tree: root = tree.getroot() return root.get('tool_path', None) return None
[docs] def data_manager_config_elems_to_xml_file(self, config_elems, config_filename): """ Persist the current in-memory list of config_elems to a file named by the value of config_filename. """ data_managers_path = self.data_managers_path if data_managers_path: root_str = '<?xml version="1.0"?><data_managers tool_path="%s"></data_managers>' % data_managers_path else: root_str = '<?xml version="1.0"?><data_managers></data_managers>' root = parse_xml_string(root_str) for elem in config_elems: root.append(elem) try: with RenamedTemporaryFile(config_filename, mode='w') as fh: fh.write(xml_to_string(root)) except Exception: log.exception("Exception in DataManagerHandler.data_manager_config_elems_to_xml_file")
[docs] def install_data_managers(self, shed_data_manager_conf_filename, metadata_dict, shed_config_dict, relative_install_dir, repository, repository_tools_tups): rval = [] if 'data_manager' in metadata_dict: tpm = tool_panel_manager.ToolPanelManager(self.app) repository_tools_by_guid = {} for tool_tup in repository_tools_tups: repository_tools_by_guid[tool_tup[1]] = dict(tool_config_filename=tool_tup[0], tool=tool_tup[2]) # Load existing data managers. try: tree, error_message = parse_xml(shed_data_manager_conf_filename, check_exists=False) except OSError as exc: if exc.errno == errno.ENOENT: with open(shed_data_manager_conf_filename, 'w') as fh: fh.write(SHED_DATA_MANAGER_CONF_XML) tree, error_message = parse_xml(shed_data_manager_conf_filename) else: raise if tree is None: return rval config_elems = [elem for elem in tree.getroot()] repo_data_manager_conf_filename = metadata_dict['data_manager'].get('config_filename', None) if repo_data_manager_conf_filename is None: log.debug("No data_manager_conf.xml file has been defined.") return rval data_manager_config_has_changes = False relative_repo_data_manager_dir = os.path.join(shed_config_dict.get('tool_path', ''), relative_install_dir) repo_data_manager_conf_filename = os.path.join(relative_repo_data_manager_dir, repo_data_manager_conf_filename) tree, error_message = parse_xml(repo_data_manager_conf_filename) if tree is None: return rval root = tree.getroot() for elem in root: if elem.tag == 'data_manager': data_manager_id = elem.get('id', None) if data_manager_id is None: log.error("A data manager was defined that does not have an id and will not be installed:\n%s" % xml_to_string(elem)) continue data_manager_dict = metadata_dict['data_manager'].get('data_managers', {}).get(data_manager_id, None) if data_manager_dict is None: log.error("Data manager metadata is not defined properly for '%s'." % (data_manager_id)) continue guid = data_manager_dict.get('guid', None) if guid is None: log.error("Data manager guid '{}' is not set in metadata for '{}'.".format(guid, data_manager_id)) continue elem.set('guid', guid) tool_guid = data_manager_dict.get('tool_guid', None) if tool_guid is None: log.error("Data manager tool guid '{}' is not set in metadata for '{}'.".format(tool_guid, data_manager_id)) continue tool_dict = repository_tools_by_guid.get(tool_guid, None) if tool_dict is None: log.error("Data manager tool guid '%s' could not be found for '%s'. Perhaps the tool is invalid?" % (tool_guid, data_manager_id)) continue tool = tool_dict.get('tool', None) if tool is None: log.error("Data manager tool with guid '%s' could not be found for '%s'. Perhaps the tool is invalid?" % (tool_guid, data_manager_id)) continue tool_config_filename = tool_dict.get('tool_config_filename', None) if tool_config_filename is None: log.error("Data manager metadata is missing 'tool_config_file' for '%s'." % (data_manager_id)) continue elem.set('shed_conf_file', shed_config_dict['config_filename']) if elem.get('tool_file', None) is not None: del elem.attrib['tool_file'] # remove old tool_file info tool_elem = tpm.generate_tool_elem(repository.tool_shed, repository.name, repository.installed_changeset_revision, repository.owner, tool_config_filename, tool, None) elem.insert(0, tool_elem) data_manager = \ self.app.data_managers.load_manager_from_elem(elem, tool_path=shed_config_dict.get('tool_path', '')) if data_manager: rval.append(data_manager) elif elem.tag is etree.Comment: pass else: log.warning("Encountered unexpected element '{}':\n{}".format(elem.tag, xml_to_string(elem))) config_elems.append(elem) data_manager_config_has_changes = True # Persist the altered shed_data_manager_config file. if data_manager_config_has_changes: reload_count = self.app.data_managers._reload_count self.data_manager_config_elems_to_xml_file(config_elems, shed_data_manager_conf_filename) while self.app.data_managers._reload_count <= reload_count: time.sleep(0.1) # Wait for shed_data_manager watcher thread to pick up changes return rval
[docs] def remove_from_data_manager(self, repository): metadata_dict = repository.metadata if metadata_dict and 'data_manager' in metadata_dict: shed_data_manager_conf_filename = self.app.config.shed_data_manager_config_file tree, error_message = parse_xml(shed_data_manager_conf_filename) if tree: root = tree.getroot() assert root.tag == 'data_managers', 'The file provided (%s) for removing data managers from is not a valid data manager xml file.' % (shed_data_manager_conf_filename) guids = [data_manager_dict.get('guid') for data_manager_dict in metadata_dict.get('data_manager', {}).get('data_managers', {}).values() if 'guid' in data_manager_dict] load_old_data_managers_by_guid = {} data_manager_config_has_changes = False config_elems = [] for elem in root: # Match Data Manager elements by guid and installed_changeset_revision elem_matches_removed_data_manager = False if elem.tag == 'data_manager': guid = elem.get('guid', None) if guid in guids: tool_elem = elem.find('tool') if tool_elem is not None: installed_changeset_revision_elem = tool_elem.find('installed_changeset_revision') if installed_changeset_revision_elem is not None: if installed_changeset_revision_elem.text == repository.installed_changeset_revision: elem_matches_removed_data_manager = True else: # This is a different version, which had been previously overridden load_old_data_managers_by_guid[guid] = elem if elem_matches_removed_data_manager: data_manager_config_has_changes = True else: config_elems.append(elem) # Remove data managers from in memory self.app.data_managers.remove_manager(guids) # Load other versions of any now uninstalled data managers, if any for elem in load_old_data_managers_by_guid.values(): self.app.data_managers.load_manager_from_elem(elem) # Persist the altered shed_data_manager_config file. if data_manager_config_has_changes: self.data_manager_config_elems_to_xml_file(config_elems, shed_data_manager_conf_filename)