def gpad2gocams(ctx, gpad_path, gpi_path, target, ontology, ttl):
# NOTE: Validation on GPAD not included here since it's currently baked into produce() above.
# Multi-param to accept multiple ontology files, then merge to one (this will make a much smaller ontology
# with only what we need, i.e. GO, RO, GOREL)
ontology_graph = OntologyFactory().create(ontology[0], ignore_cache=True)
for ont in ontology[1:]:
ontology_graph.merge(
[OntologyFactory().create(ont, ignore_cache=True)])
parser_config = assocparser.AssocParserConfig(ontology=ontology_graph,
gpi_authority_path=gpi_path)
extractor = AssocExtractor(gpad_path, parser_config=parser_config)
assocs_by_gene = extractor.group_assocs()
absolute_target = os.path.abspath(target)
gpad_basename = os.path.basename(gpad_path)
gpad_basename_root, gpad_ext = os.path.splitext(gpad_basename)
output_basename = "{}.nq".format(gpad_basename_root)
report_basename = "{}.gocamgen.report".format(gpad_basename_root)
output_path = os.path.join(absolute_target, output_basename)
report_path = os.path.join(absolute_target, report_basename)
builder = GoCamBuilder(parser_config=parser_config)
for gene, associations in assocs_by_gene.items():
if ttl:
builder.make_model_and_write_out(gene,
annotations=associations,
output_directory=absolute_target)
else:
builder.make_model_and_add_to_store(gene, annotations=associations)
if not ttl:
builder.write_out_store_to_nquads(filepath=output_path)
builder.write_report(report_filepath=report_path)
import pytest
import datetime
from ontobio.io import assocparser
from ontobio.io.gpadparser import to_association
from ontobio.ontol_factory import OntologyFactory
from ontobio.rdfgen.gocamgen import collapsed_assoc, gocam_builder, gocamgen
GO_ONTO = OntologyFactory().create(
"tests/resources/go-binding.json"
) # Placeholder ontology to instantiate models
GO_ONTO.merge([
OntologyFactory().create("tests/resources/ro-gp2term-20210723.json")
]) # Truncated RO
PARSER_CONFIG = assocparser.AssocParserConfig(
ontology=GO_ONTO,
gpi_authority_path="tests/resources/mgi2.test_entities.gpi")
def test_evidence_max_date():
ev1 = gocamgen.GoCamEvidence(code="ECO:0000314",
references=["PMID:12345"],
date="2008-08-14")
ev2 = gocamgen.GoCamEvidence(code="ECO:0000314",
references=["PMID:12345"],
date="2011-04-12")
ev3 = gocamgen.GoCamEvidence(code="ECO:0000314",
references=["PMID:12345"],
date="2021-03-01")
max_date = gocamgen.GoCamEvidence.sort_date([ev1, ev2, ev3])[-1]
assert max_date == "2021-03-01"
