import re
import schema_salad.schema
import schema_salad.jsonld_context
import json

metadataSchema = '$(inputs.metadataSchema.path)'
metadata = $(inputs.metadata)
subjects = $(inputs.subjects)
dups = json.loads('''$(inputs.dups)''')
originalLabels = $(inputs.originalLabels)

(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"))

import logging

if dups:
    sameseqs = open(dups["path"], "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["path"], "rt")
print(orig.read())