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 write_assocs(assocs, outfile, args):
w = None
fmt = args.to.lower()
version = args.version
if fmt is None or fmt == 'gaf':
if version:
w = GafWriter(file=outfile, version=args.version)
else:
w = GafWriter(file=outfile)
elif fmt == 'gpad':
if version:
w = GpadWriter(file=outfile, version=args.version)
else:
w = GpadWriter(file=outfile)
else:
raise ValueError("Not supported: {}".format(fmt))
w.write(assocs)
def write_assocs(assocs, outfile, args):
w = GpadWriter()
fmt = args.to
if fmt is None or fmt == 'gaf':
w = GafWriter()
elif fmt == 'gpad':
w = GpadWriter()
else:
raise ValueError("Not supported: {}".format(fmt))
w.file = outfile
w.write(assocs)
def convert_assocs(ont, file, outfile, p, args):
assocs = p.parse(open(file, "r"), None)
w = GpadWriter()
fmt = args.to
if fmt == 'gpad':
w = GpadWriter()
else:
raise ValueError("Not supported: {}".format(fmt))
w.file = outfile
w.write(assocs)
def test_convert_gaf_to_gpad():
p = GafParser()
p.config.ecomap = EcoMap()
w = GpadWriter()
p2 = GpadParser()
convert(POMBASE, p, w, p2)