def load_from_element(self, elem, tool_path):
assert (
elem.tag == "data_manager"
), 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % (elem.tag)
self.declared_id = elem.get("id", None)
self.guid = elem.get("guid", None)
path = elem.get("tool_file", None)
self.version = elem.get("version", self.version)
tool_shed_repository_id = None
tool_guid = None
if path is None:
tool_elem = elem.find("tool")
assert tool_elem is not None, (
"Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s"
% (util.xml_to_string(elem))
)
path = tool_elem.get("file", None)
tool_guid = tool_elem.get("guid", None)
# need to determine repository info so that dependencies will work correctly
tool_shed = tool_elem.find("tool_shed").text
repository_name = tool_elem.find("repository_name").text
repository_owner = tool_elem.find("repository_owner").text
installed_changeset_revision = tool_elem.find("installed_changeset_revision").text
# save repository info here
self.tool_shed_repository_info_dict = dict(
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision,
)
# get tool_shed repo id
tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision(
self.data_managers.app, tool_shed, repository_name, repository_owner, installed_changeset_revision
)
if tool_shed_repository is None:
log.warning(
"Could not determine tool shed repository from database. This should only ever happen when running tests."
)
# we'll set tool_path manually here from shed_conf_file
tool_shed_repository_id = None
try:
tool_path = util.parse_xml(elem.get("shed_conf_file")).getroot().get("tool_path", tool_path)
except Exception, e:
log.error("Error determining tool_path for Data Manager during testing: %s", e)
else:
tool_shed_repository_id = self.data_managers.app.security.encode_id(tool_shed_repository.id)
# use shed_conf_file to determine tool_path
shed_conf_file = elem.get("shed_conf_file", None)
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename(shed_conf_file, None)
if shed_conf:
tool_path = shed_conf.get("tool_path", tool_path)
def load_from_element( self, elem, tool_path ):
assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % ( elem.tag )
self.declared_id = elem.get( 'id', None )
self.guid = elem.get( 'guid', None )
path = elem.get( 'tool_file', None )
self.version = elem.get( 'version', self.version )
tool_shed_repository_id = None
tool_guid = None
if path is None:
tool_elem = elem.find( 'tool' )
assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % ( util.xml_to_string( elem ) )
path = tool_elem.get( "file", None )
tool_guid = tool_elem.get( "guid", None )
#need to determine repository info so that dependencies will work correctly
tool_shed_url = tool_elem.find( 'tool_shed' ).text
# Handle protocol changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.data_managers.app, tool_shed_url )
# The protocol is not stored in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
repository_name = tool_elem.find( 'repository_name' ).text
repository_owner = tool_elem.find( 'repository_owner' ).text
installed_changeset_revision = tool_elem.find( 'installed_changeset_revision' ).text
self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
tool_shed_repository = \
suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.data_managers.app,
tool_shed,
repository_name,
repository_owner,
installed_changeset_revision )
if tool_shed_repository is None:
log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' )
#we'll set tool_path manually here from shed_conf_file
tool_shed_repository_id = None
try:
tool_path = util.parse_xml( elem.get( 'shed_conf_file' ) ).getroot().get( 'tool_path', tool_path )
except Exception, e:
log.error( 'Error determining tool_path for Data Manager during testing: %s', e )
else:
tool_shed_repository_id = self.data_managers.app.security.encode_id( tool_shed_repository.id )
#use shed_conf_file to determine tool_path
shed_conf_file = elem.get( "shed_conf_file", None )
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename( shed_conf_file, None )
if shed_conf:
tool_path = shed_conf.get( "tool_path", tool_path )
def load_from_element(self, elem, tool_path):
assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % (
elem.tag)
self.declared_id = elem.get('id', None)
self.guid = elem.get('guid', None)
path = elem.get('tool_file', None)
self.version = elem.get('version', self.version)
tool_shed_repository_id = None
tool_guid = None
if path is None:
tool_elem = elem.find('tool')
assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % (
util.xml_to_string(elem))
path = tool_elem.get("file", None)
tool_guid = tool_elem.get("guid", None)
#need to determine repository info so that dependencies will work correctly
tool_shed_url = tool_elem.find('tool_shed').text
# Handle protocol changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
self.data_managers.app, tool_shed_url)
# The protocol is not stored in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url(
tool_shed_url)
repository_name = tool_elem.find('repository_name').text
repository_owner = tool_elem.find('repository_owner').text
installed_changeset_revision = tool_elem.find(
'installed_changeset_revision').text
self.tool_shed_repository_info_dict = dict(
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision)
tool_shed_repository = \
suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.data_managers.app,
tool_shed,
repository_name,
repository_owner,
installed_changeset_revision )
if tool_shed_repository is None:
log.warning(
'Could not determine tool shed repository from database. This should only ever happen when running tests.'
)
#we'll set tool_path manually here from shed_conf_file
tool_shed_repository_id = None
try:
tool_path = util.parse_xml(
elem.get('shed_conf_file')).getroot().get(
'tool_path', tool_path)
except Exception, e:
log.error(
'Error determining tool_path for Data Manager during testing: %s',
e)
else:
tool_shed_repository_id = self.data_managers.app.security.encode_id(
tool_shed_repository.id)
#use shed_conf_file to determine tool_path
shed_conf_file = elem.get("shed_conf_file", None)
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename(
shed_conf_file, None)
if shed_conf:
tool_path = shed_conf.get("tool_path", tool_path)
def load_from_element(self, elem, tool_path):
assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % (
root.tag)
self.declared_id = elem.get('id', None)
self.guid = elem.get('guid', None)
path = elem.get('tool_file', None)
self.version = elem.get('version', self.version)
tool_shed_repository_id = None
tool_guid = None
if path is None:
tool_elem = elem.find('tool')
assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % (
util.xml_to_string(elem))
path = tool_elem.get("file", None)
tool_guid = tool_elem.get("guid", None)
#need to determine repository info so that dependencies will work correctly
tool_shed = tool_elem.find('tool_shed').text
repository_name = tool_elem.find('repository_name').text
repository_owner = tool_elem.find('repository_owner').text
installed_changeset_revision = tool_elem.find(
'installed_changeset_revision').text
#save repository info here
self.tool_shed_repository_info_dict = dict(
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision)
#get tool_shed repo id
tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision(
self.data_managers.app, tool_shed, repository_name,
repository_owner, installed_changeset_revision)
tool_shed_repository_id = self.data_managers.app.security.encode_id(
tool_shed_repository.id)
#use shed_conf_file to determine tool_path
shed_conf_file = elem.get("shed_conf_file", None)
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename(
shed_conf_file, None)
if shed_conf:
tool_path = shed_conf.get("tool_path", tool_path)
assert path is not None, "A tool file path could not be determined:\n%s" % (
util.xml_to_string(elem))
self.load_tool(os.path.join(tool_path, path),
guid=tool_guid,
data_manager_id=self.id,
tool_shed_repository_id=tool_shed_repository_id)
self.name = elem.get('name', self.tool.name)
self.description = elem.get('description', self.tool.description)
for data_table_elem in elem.findall('data_table'):
data_table_name = data_table_elem.get("name")
assert data_table_name is not None, "A name is required for a data table entry"
if data_table_name not in self.data_tables:
self.data_tables[data_table_name] = odict() #{}
output_elem = data_table_elem.find('output')
if output_elem is not None:
for column_elem in output_elem.findall('column'):
column_name = column_elem.get('name', None)
assert column_name is not None, "Name is required for column entry"
data_table_coumn_name = column_elem.get(
'data_table_name', column_name)
self.data_tables[data_table_name][
data_table_coumn_name] = column_name
output_ref = column_elem.get('output_ref', None)
if output_ref is not None:
if data_table_name not in self.output_ref_by_data_table:
self.output_ref_by_data_table[data_table_name] = {}
self.output_ref_by_data_table[data_table_name][
data_table_coumn_name] = output_ref
value_translation_elems = column_elem.findall(
'value_translation')
if value_translation_elems is not None:
for value_translation_elem in value_translation_elems:
value_translation = value_translation_elem.text
if value_translation is not None:
value_translation_type = value_translation_elem.get(
'type', DEFAULT_VALUE_TRANSLATION_TYPE)
if data_table_name not in self.value_translation_by_data_table_column:
self.value_translation_by_data_table_column[
data_table_name] = {}
if data_table_coumn_name not in self.value_translation_by_data_table_column[
data_table_name]:
self.value_translation_by_data_table_column[
data_table_name][
data_table_coumn_name] = []
if value_translation_type == 'function':
if value_translation in VALUE_TRANSLATION_FUNCTIONS:
value_translation = VALUE_TRANSLATION_FUNCTIONS[
value_translation]
else:
raise ValueError(
"Unsupported value translation function: '%s'"
% (value_translation))
else:
assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError(
"Unsupported value translation type: '%s'"
% (value_translation_type))
self.value_translation_by_data_table_column[
data_table_name][
data_table_coumn_name].append(
value_translation)
for move_elem in column_elem.findall('move'):
move_type = move_elem.get('type', 'directory')
relativize_symlinks = move_elem.get(
'relativize_symlinks', False
) #TODO: should we instead always relativize links?
source_elem = move_elem.find('source')
if source_elem is None:
source_base = None
source_value = ''
else:
source_base = source_elem.get('base', None)
source_value = source_elem.text
target_elem = move_elem.find('target')
if target_elem is None:
target_base = None
target_value = ''
else:
target_base = target_elem.get('base', None)
target_value = target_elem.text
if data_table_name not in self.move_by_data_table_column:
self.move_by_data_table_column[
data_table_name] = {}
self.move_by_data_table_column[data_table_name][
data_table_coumn_name] = dict(
type=move_type,
source_base=source_base,
source_value=source_value,
target_base=target_base,
target_value=target_value,
relativize_symlinks=relativize_symlinks)
def load_from_element(self, elem, tool_path):
assert (
elem.tag == "data_manager"
), 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % (root.tag)
self.declared_id = elem.get("id", None)
self.guid = elem.get("guid", None)
path = elem.get("tool_file", None)
self.version = elem.get("version", self.version)
tool_shed_repository_id = None
tool_guid = None
if path is None:
tool_elem = elem.find("tool")
assert tool_elem is not None, (
"Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s"
% (util.xml_to_string(elem))
)
path = tool_elem.get("file", None)
tool_guid = tool_elem.get("guid", None)
# need to determine repository info so that dependencies will work correctly
tool_shed = tool_elem.find("tool_shed").text
repository_name = tool_elem.find("repository_name").text
repository_owner = tool_elem.find("repository_owner").text
installed_changeset_revision = tool_elem.find("installed_changeset_revision").text
# save repository info here
self.tool_shed_repository_info_dict = dict(
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision,
)
# get tool_shed repo id
tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision(
self.data_managers.app, tool_shed, repository_name, repository_owner, installed_changeset_revision
)
tool_shed_repository_id = self.data_managers.app.security.encode_id(tool_shed_repository.id)
# use shed_conf_file to determine tool_path
shed_conf_file = elem.get("shed_conf_file", None)
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename(shed_conf_file, None)
if shed_conf:
tool_path = shed_conf.get("tool_path", tool_path)
assert path is not None, "A tool file path could not be determined:\n%s" % (util.xml_to_string(elem))
self.load_tool(
os.path.join(tool_path, path),
guid=tool_guid,
data_manager_id=self.id,
tool_shed_repository_id=tool_shed_repository_id,
)
self.name = elem.get("name", self.tool.name)
self.description = elem.get("description", self.tool.description)
for data_table_elem in elem.findall("data_table"):
data_table_name = data_table_elem.get("name")
assert data_table_name is not None, "A name is required for a data table entry"
if data_table_name not in self.data_tables:
self.data_tables[data_table_name] = odict() # {}
output_elem = data_table_elem.find("output")
if output_elem is not None:
for column_elem in output_elem.findall("column"):
column_name = column_elem.get("name", None)
assert column_name is not None, "Name is required for column entry"
data_table_coumn_name = column_elem.get("data_table_name", column_name)
self.data_tables[data_table_name][data_table_coumn_name] = column_name
output_ref = column_elem.get("output_ref", None)
if output_ref is not None:
if data_table_name not in self.output_ref_by_data_table:
self.output_ref_by_data_table[data_table_name] = {}
self.output_ref_by_data_table[data_table_name][data_table_coumn_name] = output_ref
value_translation_elems = column_elem.findall("value_translation")
if value_translation_elems is not None:
for value_translation_elem in value_translation_elems:
value_translation = value_translation_elem.text
if value_translation is not None:
value_translation_type = value_translation_elem.get(
"type", DEFAULT_VALUE_TRANSLATION_TYPE
)
if data_table_name not in self.value_translation_by_data_table_column:
self.value_translation_by_data_table_column[data_table_name] = {}
if (
data_table_coumn_name
not in self.value_translation_by_data_table_column[data_table_name]
):
self.value_translation_by_data_table_column[data_table_name][
data_table_coumn_name
] = []
if value_translation_type == "function":
if value_translation in VALUE_TRANSLATION_FUNCTIONS:
value_translation = VALUE_TRANSLATION_FUNCTIONS[value_translation]
else:
raise ValueError(
"Unsupported value translation function: '%s'" % (value_translation)
)
else:
assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError(
"Unsupported value translation type: '%s'" % (value_translation_type)
)
self.value_translation_by_data_table_column[data_table_name][
data_table_coumn_name
].append(value_translation)
for move_elem in column_elem.findall("move"):
move_type = move_elem.get("type", "directory")
relativize_symlinks = move_elem.get(
"relativize_symlinks", False
) # TODO: should we instead always relativize links?
source_elem = move_elem.find("source")
if source_elem is None:
source_base = None
source_value = ""
else:
source_base = source_elem.get("base", None)
source_value = source_elem.text
target_elem = move_elem.find("target")
if target_elem is None:
target_base = None
target_value = ""
else:
target_base = target_elem.get("base", None)
target_value = target_elem.text
if data_table_name not in self.move_by_data_table_column:
self.move_by_data_table_column[data_table_name] = {}
self.move_by_data_table_column[data_table_name][data_table_coumn_name] = dict(
type=move_type,
source_base=source_base,
source_value=source_value,
target_base=target_base,
target_value=target_value,
relativize_symlinks=relativize_symlinks,
)
