def produce_ttl(dataset, target_dir, gaf_path, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(
ontology=ontology_graph
)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
ttl_path = os.path.join(os.path.split(gaf_path)[0], "{}_cam.ttl".format(dataset))
click.echo("Producing ttl: {}".format(ttl_path))
rdf_writer = assoc_rdfgen.TurtleRdfWriter()
transformer = assoc_rdfgen.CamRdfTransform(writer=rdf_writer)
parser_config = assocparser.AssocParserConfig(ontology=ontology_graph)
with open(gaf_path) as gf:
with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations:
for association in associations:
if "header" not in association or not association["header"]:
transformer.provenance()
transformer.translate(association)
with open(ttl_path, "wb") as ttl:
click.echo("Writing ttl to disk")
rdf_writer.serialize(destination=ttl)
return ttl_path
def make_products(dataset, target_dir, gaf_path, products, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(
ontology=ontology_graph,
paint=True
)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
product_files = {
"gpad": open(os.path.join(os.path.split(gaf_path)[0], "{}.gpad".format(dataset)), "w"),
"ttl": open(os.path.join(os.path.split(gaf_path)[0], "{}_cam.ttl".format(dataset)), "wb")
}
if not products["gpad"] and not products["ttl"]:
# Bail if we have no products
return []
# def write_gpi_entity(association, bridge, gpiwriter):
with open(gaf_path) as gf:
# gpi info:
click.echo("Using {} as the gaf to build data products with".format(gaf_path))
if products["ttl"]:
click.echo("Setting up {}".format(product_files["ttl"].name))
rdf_writer = assoc_rdfgen.TurtleRdfWriter(label=os.path.split(product_files["ttl"].name)[1] )
transformer = assoc_rdfgen.CamRdfTransform(writer=rdf_writer)
parser_config = assocparser.AssocParserConfig(ontology=ontology_graph)
if products["gpad"]:
click.echo("Setting up {}".format(product_files["gpad"].name))
gpadwriter = GpadWriter(file=product_files["gpad"])
click.echo("Making products...")
with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations:
for association in associations:
if products["ttl"]:
if "header" not in association or not association["header"]:
transformer.provenance()
transformer.translate(association)
if products["gpad"]:
gpadwriter.write_assoc(association)
# post ttl steps
if products["ttl"]:
click.echo("Writing ttl to disk")
rdf_writer.serialize(destination=product_files["ttl"])
# After we run through associations
for f in product_files.values():
f.close()
return [product_files[prod].name for prod in sorted(product_files.keys()) if products[prod]]
def convert(association, ontology, output, association_file):
click.echo("converting {}".format(association))
rdfWriter = assoc_rdfgen.TurtleRdfWriter()
rdfTransformer = assoc_rdfgen.CamRdfTransform(writer=rdfWriter)
parser_config = assocparser.AssocParserConfig(
ontology=make_ontology(ontology))
parser = _association_parser(association, parser_config)
associations = parser.association_generator(file=association_file)
for assoc in associations:
rdfTransformer.provenance()
rdfTransformer.translate(assoc)
rdfWriter.serialize(destination=output)
def convert(association, ontology, output, association_file):
click.echo("converting {}".format(association))
rdfWriter = assoc_rdfgen.TurtleRdfWriter(
label=os.path.basename(output.name))
rdfTransformer = assoc_rdfgen.CamRdfTransform(writer=rdfWriter)
parser_config = assocparser.AssocParserConfig(
ontology=make_ontology(ontology))
parser = _association_parser(association, parser_config)
with open(association_file) as af:
lines = sum(1 for line in af)
with open(association_file) as af:
associations = parser.association_generator(file=af)
with click.progressbar(iterable=associations, length=lines) as assocs:
for assoc in assocs:
rdfTransformer.provenance()
rdfTransformer.translate(assoc)
click.echo("Writing ttl to disk")
rdfWriter.serialize(destination=output)