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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 (
etree,
parse_xml_string,
xml_to_string,
)
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"?>
<data_managers>
</data_managers>
"""
[docs]class DataManagerHandler:
@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(f"Data manager guid '{guid}' is not set in metadata for '{data_manager_id}'.")
continue
elem.set('guid', guid)
tool_guid = data_manager_dict.get('tool_guid', None)
if tool_guid is None:
log.error(f"Data manager tool guid '{tool_guid}' is not set in metadata for '{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)