import os
from typing import Optional, Union
from collections import defaultdict
from linkml_runtime.dumpers.yaml_dumper import YAMLDumper
from linkml_runtime.dumpers.json_dumper import JSONDumper
from linkml_runtime.dumpers.rdf_dumper import RDFDumper
from linkml_runtime.dumpers.rdflib_dumper import RDFLibDumper
from linkml_runtime.dumpers.csv_dumper import CSVDumper
from linkml_runtime.loaders.yaml_loader import YAMLLoader
from linkml_runtime.loaders.json_loader import JSONLoader
from linkml_runtime.loaders.rdf_loader import RDFLoader
from linkml_runtime.loaders.rdflib_loader import RDFLibLoader
from linkml_runtime.loaders.csv_loader import CSVLoader
from linkml_runtime.loaders.loader_root import Loader
from linkml_runtime.utils.schemaview import SchemaView
from linkml_runtime.linkml_model.meta import ClassDefinitionName, SlotDefinitionName, SchemaDefinition
from linkml_runtime.utils.yamlutils import YAMLRoot
from linkml.generators.jsonldcontextgen import ContextGenerator
dumpers_loaders = {
'yaml': (YAMLDumper, YAMLLoader),
'json': (JSONDumper, JSONLoader),
'rdf': (RDFLibDumper, RDFLibLoader),
'ttl': (RDFLibDumper, RDFLibLoader),
'json-ld': (RDFLibDumper, RDFLibLoader),
'csv': (CSVDumper, CSVLoader),
'tsv': (CSVDumper, CSVLoader),
}
aliases = {
'ttl': 'rdf',
'jsonld': 'json-ld',
}
def _get_format(path: str, specified_format: str =None, default=None):
if specified_format is None:
if path is None:
if default is None:
raise Exception(f'Must pass format option OR pass a filename with known file suffix')
else:
specified_format = default
else:
_, ext = os.path.splitext(path)
if ext is not None:
specified_format = ext.replace('.', '')
else:
raise Exception(f'Must pass format option OR use known file suffix: {path}')
specified_format = specified_format.lower()
if specified_format in aliases:
specified_format = aliases[specified_format]
return specified_format
def _is_xsv(fmt: str) -> bool:
return fmt == 'csv' or fmt == 'tsv'
def _is_rdf_format(fmt: str) -> bool:
return fmt == 'rdf' or fmt == 'ttl' or fmt == 'json-ld'
[docs]def get_loader(fmt: str) -> Loader:
return dumpers_loaders[fmt][1]()
[docs]def get_dumper(fmt: str) -> Loader:
return dumpers_loaders[fmt][0]()
def _get_context(schema) -> str:
return ContextGenerator(schema).serialize()
[docs]def infer_root_class(sv: SchemaView) -> Optional[ClassDefinitionName]:
"""
Infer the class that should be at the root of the object tree
(Note this is distinct from the root of the class hierarchy)
If a class is explicitly designated with tree_root, use this.
Otherwise use the class that is not referenced as a range in any other class.
"""
for c in sv.all_classes().values():
if c.tree_root:
return c.name
refs = defaultdict(int)
for cn in sv.all_class().keys():
for sn in sv.class_slots(cn):
slot = sv.induced_slot(sn, cn)
r = slot.range
if r in sv.all_class():
for a in sv.class_ancestors(r):
refs[a] += 1
candidates = [cn for cn in sv.all_class().keys() if cn not in refs]
# throw Exception if unambiguous root cannot be inferred
if len(candidates) > 1:
raise RuntimeError(f"Multiple potential target classes found: {candidates}. "
"Please specify a target using --target_class or by adding "
"tree_root: true to the relevant class in the schema.")
if len(candidates) == 1:
return candidates[0]
else:
return None
[docs]def infer_index_slot(sv: SchemaView, root_class: ClassDefinitionName) -> Optional[SlotDefinitionName]:
index_slots = []
for sn in sv.class_slots(root_class):
slot = sv.induced_slot(sn, root_class)
if slot.multivalued and slot.range in sv.all_class():
index_slots.append(sn)
if len(index_slots) == 1:
return index_slots[0]
else:
return None