Merge branch 'master' into patch-3

1 files changed, 36 insertions, 4 deletions

diff --git a/workflows/pangenome-generate/merge-metadata.py b/workflows/pangenome-generate/merge-metadata.py
index 64275b1..65d08a6 100644
--- a/workflows/pangenome-generate/merge-metadata.py
+++ b/workflows/pangenome-generate/merge-metadata.py
@@ -1,9 +1,28 @@
+import re
 import schema_salad.schema
 import schema_salad.jsonld_context
+import json
+import sys
+import os
+import logging
 
-metadataSchema = '$(inputs.metadataSchema.path)'
-metadata = $(inputs.metadata)
-subjects = $(inputs.subjects)
+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,
@@ -11,7 +30,20 @@ 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"))
+
+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())