def __init__(self, folder_path, use_db_metadata_classes=None, use_edge_metadata_classes=None):
gcConst.O_FILE_PATH = os.path.join(folder_path, gcConst.O_FILE_FOLDER_NAME)
gcConst.IN_FILE_PATH = os.path.join(folder_path, gcConst.IN_FILE_FOLDER_NAME)
self.db_file_metadata = [x() for x in utils.get_leaf_subclasses(DbMetadata)]
self.file_readers = [x() for x in utils.get_leaf_subclasses(FileReader)]
self.file_processors = [x() for x in utils.get_leaf_subclasses(FileProcessor)]
self.infile_metadata = [x() for x in utils.get_leaf_subclasses(InfileMetadata)]
self.edge_metadata = [x(graphProp.QUALITY) for x in utils.get_leaf_subclasses(EdgeRegularMetadata)] + [
x(graphProp.QUALITY) for x in utils.get_leaf_subclasses(EdgeOntoMetadata)
]
self.tn_edge_metadata = [x(graphProp.QUALITY) for x in utils.get_leaf_subclasses(TnEdgeRegularMetadata)]
self.dbType_reader_map = utils.cls_list_to_dic(self.file_readers, "dbType")
self.readerType_processor_map = utils.cls_list_to_dic(self.file_processors, "readerType")
self.infileType_inMetadata_map = {x.infileType: x for x in self.infile_metadata}
# if not glob.DIRECTED:
## remove onto
# if use_edge_metadata_classes is None:
# use_edge_metadata_classes = [x(glob.QUALITY) for x in utils.get_leaf_subclasses(EdgeRegularMetadata)]
# else:
# temp_use_edge_metadata_classes =[]
# for edge_class in use_edge_metadata_classes:
# if inspect.isclass(edge_class):
# if not issubclass(edge_class, EdgeOntoMetadata):
# temp_use_edge_metadata_classes.append(edge_class())
# else:
# if not issubclass(type(edge_class), EdgeOntoMetadata):
# temp_use_edge_metadata_classes.append(edge_class)
# use_edge_metadata_classes = temp_use_edge_metadata_classes
# #use_edge_metadata_classes = [x for x in use_edge_metadata_classes if not issubclass(type(x), EdgeOntoMetadata)]
# use only the desired sources
if use_db_metadata_classes is not None:
self.init_custom_sources_bottom_up(use_db_metadata_classes)
if use_edge_metadata_classes is not None:
self.init_custom_sources_top_down(use_edge_metadata_classes)
graphProp.EDGE_TYPES = [str(x.__class__.__name__) for x in self.edge_metadata]
def init_custom_sources_top_down(self, use_edge_metdata_classes):
"""hepler __init__ function for custom edge_metadata_classes"""
# remove edge_metadata
logging.info("Edge Metadata removed: " + str([
x.__class__.__name__
for x in self.edge_metadata if x.EDGE_INMETA_CLASS not in
[y.EDGE_INMETA_CLASS for y in use_edge_metdata_classes]
]))
self.edge_metadata = []
for x in use_edge_metdata_classes:
if inspect.isclass(x):
self.edge_metadata.append(x())
else:
self.edge_metadata.append(x)
# remove inMetadata
infileType_edgeMetadata_map = utils.cls_list_to_dic(
self.edge_metadata, "EDGE_INMETA_CLASS.INFILE_TYPE")
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(self.edge_metadata,
"MAP1_META_CLASS.INFILE_TYPE",
lambda a: a.MAP1_META_CLASS is not None))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(self.edge_metadata,
"MAP2_META_CLASS.INFILE_TYPE",
lambda a: a.MAP2_META_CLASS is not None))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(
self.edge_metadata, "MAP1_ALT_ID_META_CLASS.INFILE_TYPE",
lambda a: a.MAP1_ALT_ID_META_CLASS is not None))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(
self.edge_metadata, "MAP2_ALT_ID_META_CLASS.INFILE_TYPE",
lambda a: a.MAP2_ALT_ID_META_CLASS is not None))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(self.tn_edge_metadata,
"EDGE_INMETA_CLASS.INFILE_TYPE"))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(self.tn_edge_metadata,
"MAP1_META_CLASS.INFILE_TYPE",
lambda a: a.MAP1_META_CLASS is not None))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(self.tn_edge_metadata,
"MAP2_META_CLASS.INFILE_TYPE",
lambda a: a.MAP2_META_CLASS is not None))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(
self.tn_edge_metadata,
"MAP1_ALT_ID_META_CLASS.INFILE_TYPE",
lambda a: a.MAP1_ALT_ID_META_CLASS is not None,
))
infileType_edgeMetadata_map.update(
utils.cls_list_to_dic(
self.tn_edge_metadata,
"MAP2_ALT_ID_META_CLASS.INFILE_TYPE",
lambda a: a.MAP2_ALT_ID_META_CLASS is not None,
))
keep_infileTypes = list(infileType_edgeMetadata_map.keys())
logging.info("Infile Metadata removed: " + str([
x.__class__.__name__ for x in self.infile_metadata
if x.infileType not in keep_infileTypes
]))
self.infile_metadata = [
x for x in self.infile_metadata if x.infileType in keep_infileTypes
]
self.infileType_inMetadata_map = {
x.infileType: x
for x in self.infile_metadata
}
# remove processors
logging.info("Processors removed: " + str([
x.__class__.__name__ for x in self.file_processors
if x.infileType not in keep_infileTypes
]))
self.file_processors = [
x for x in self.file_processors if x.infileType in keep_infileTypes
]
self.readerType_processor_map = utils.cls_list_to_dic(
self.file_processors, "readerType")
# remove readers
keep_readerType = list(self.readerType_processor_map.keys())
logging.info("Readers removed: " + str([
x.__class__.__name__
for x in self.file_readers if x.readerType not in keep_readerType
]))
self.file_readers = [
x for x in self.file_readers if x.readerType in keep_readerType
]
self.dbType_reader_map = utils.cls_list_to_dic(self.file_readers,
"dbType")
# remove db_metadata
keep_dbType = list(self.dbType_reader_map.keys())
logging.info("DB_source removed: " + str([
x.__class__.__name__
for x in self.db_file_metadata if x.dbType not in keep_dbType
]))
self.db_file_metadata = [
x for x in self.db_file_metadata if x.dbType in keep_dbType
]
def init_custom_sources_bottom_up(self, use_db_metdata_classes):
"""helper __init__ function for custom db_metadata_classes"""
self.db_file_metadata = []
# remove dbMetadata from list
# make sure to use instances of classes
for x in use_db_metdata_classes:
if inspect.isclass(x):
self.db_file_metadata.append(x())
else:
self.db_file_metadata.append(x)
# remove readers
keep_dbType = [x.dbType for x in self.db_file_metadata]
logging.info("readers removed: " + str([
x.__class__.__name__
for x in self.file_readers if x.dbType not in keep_dbType
]))
self.file_readers = [
x for x in self.file_readers if x.dbType in keep_dbType
]
self.dbType_reader_map = utils.cls_list_to_dic(self.file_readers,
"dbType")
# remove processors
keep_readerType = [x.readerType for x in self.file_readers]
logging.info("processors removed: %s" % (str([
x.__class__.__name__ for x in self.file_processors
if x.readerType not in keep_readerType
])))
self.file_processors = [
x for x in self.file_processors if x.readerType in keep_readerType
]
self.readerType_processor_map = utils.cls_list_to_dic(
self.file_processors, "readerType")
# remove infile metadata
keep_infileType = [x.infileType for x in self.file_processors]
logging.info("processors removed: " + str([
x.__class__.__name__ for x in self.infile_metadata
if x.infileType not in keep_infileType
]))
self.infile_metadata = [
x for x in self.infile_metadata if x.infileType in keep_infileType
]
self.infileType_inMetadata_map = {
x.infileType: x
for x in self.infile_metadata
}
# remove edge metadata
logging.info("edges removed: " + str([
x.__class__.__name__
for x in self.edge_metadata + self.tn_edge_metadata
if x.EDGE_INMETA_CLASS.INFILE_TYPE not in keep_infileType
]))
self.edge_metadata = [
x for x in self.edge_metadata
if x.EDGE_INMETA_CLASS.INFILE_TYPE in keep_infileType
]
self.tn_edge_metadata = [
x for x in self.tn_edge_metadata
if x.EDGE_INMETA_CLASS.INFILE_TYPE in keep_infileType
]
# check for deleted dependencies of mappings
additional_remove_metaEdges = []
additional_remove_mapping_infileType = []
for metaEdge in self.edge_metadata + self.tn_edge_metadata:
mappings = [
metaEdge.MAP1_META_CLASS,
metaEdge.MAP2_META_CLASS,
metaEdge.MAP1_ALT_ID_META_CLASS,
metaEdge.MAP2_ALT_ID_META_CLASS,
]
for mapping in mappings:
if mapping is not None and mapping.INFILE_TYPE not in keep_infileType:
additional_remove_metaEdges.append(metaEdge)
additional_remove_mapping_infileType.append(
mapping.INFILE_TYPE)
if len(additional_remove_metaEdges) > 0:
message = (
"\nDue to manual exclusion of DB resources, also the edges: %s\n "
"will be removed due to deleted dependencies of used mappings (i.e. %s\n "
"Consider manually exclude edges instead of DB resources." % (
str([
x.__class__.__name__
for x in additional_remove_metaEdges
]),
str([str(x)
for x in additional_remove_mapping_infileType]),
))
logging.warning(message)
if globConst.GUI_MODE:
from openbiolink.gui import gui
gui.askForExit(message)
elif globConst.INTERACTIVE_MODE:
Cli.ask_for_exit(message)
else:
sys.exit()
self.edge_metadata = [
x for x in self.edge_metadata
if x not in additional_remove_metaEdges
]
self.tn_edge_metadata = [
x for x in self.tn_edge_metadata
if x not in additional_remove_metaEdges
]