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-rw-r--r--workflows/pangenome-generate/merge-metadata.py21
1 files changed, 20 insertions, 1 deletions
diff --git a/workflows/pangenome-generate/merge-metadata.py b/workflows/pangenome-generate/merge-metadata.py
index 64275b1..bfec781 100644
--- a/workflows/pangenome-generate/merge-metadata.py
+++ b/workflows/pangenome-generate/merge-metadata.py
@@ -1,9 +1,13 @@
+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,
@@ -11,7 +15,22 @@ subjects = $(inputs.subjects)
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"], True)
+ 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())