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import re
import schema_salad.schema
import schema_salad.jsonld_context
import json
import sys
import os
import logging
metadataSchema = sys.argv[1]
originalLabels = sys.argv[2]
dups = None
if len(sys.argv) == 4:
dups = sys.argv[3]
def readitems(stem):
items = []
b = 1
while os.path.exists("%s%i" % (stem, b)):
with open("%s%i" % (stem, b)) as f:
items.extend(json.load(f))
b += 1
return items
metadata = readitems("block")
subjects = readitems("subs")
(document_loader,
avsc_names,
schema_metadata,
metaschema_loader) = schema_salad.schema.load_schema(metadataSchema)
for i, m in enumerate(metadata):
doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, m["path"], False, False)
doc["id"] = subjects[i]
g = schema_salad.jsonld_context.makerdf(subjects[i], doc, document_loader.ctx)
print(g.serialize(format="ntriples").decode("utf-8"))
if dups:
sameseqs = open(dups, "rt")
for d in sameseqs:
logging.warn(d)
g = re.match(r"\d+\t(.*)", d)
logging.warn("%s", g.group(1))
sp = g.group(1).split(",")
for n in sp[1:]:
print("<%s> <http://biohackathon.org/bh20-seq-schema/has_duplicate_sequence> <%s> ." % (n.strip(), sp[0].strip()))
orig = open(originalLabels, "rt")
print(orig.read())
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