From c01188ec20936462357b317f81567aadc64c8f33 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 10 Nov 2020 11:52:37 -0500
Subject: Use arvados uuids for RDF subjects.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 bh20simplewebuploader/main.py                | 5 +++++
 workflows/pangenome-generate/collect-seqs.py | 5 ++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 51048a4..bcdf8d8 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -695,6 +695,11 @@ union
    <http://covid19.genenetwork.org/resource/{id}> pubseq:sample ?sample .
    ?sequenceuri pubseq:sample ?sample .
 }}
+union
+{{
+   ?sequenceuri <http://biohackathon.org/bh20-seq-schema/collection_pdh> "{id}" .
+   ?sequenceuri pubseq:sample ?sample .
+}}
 
    ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
    ?geo rdfs:label ?geoname .
diff --git a/workflows/pangenome-generate/collect-seqs.py b/workflows/pangenome-generate/collect-seqs.py
index 1a0807c..225a61f 100644
--- a/workflows/pangenome-generate/collect-seqs.py
+++ b/workflows/pangenome-generate/collect-seqs.py
@@ -36,11 +36,14 @@ if len(sys.argv) > 3:
 
 for item in validated:
     pdh = item["portable_data_hash"]
+    uuid = item["uuid"]
     with arvados.collection.CollectionReader(pdh, api_client=api, keep_client=keepclient) as col:
         with col.open("sequence.fasta", "rt") as fa:
-            subject = "http://covid19.genenetwork.org/resource/%s" % pdh
+            subject = "http://covid19.genenetwork.org/resource/%s" % uuid
             label = fa.readline().strip()
             merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subject, label[1:].replace('"', '\\"')))
+            merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/collection_pdh> \"%s\" .\n" % (subject, pdh))
+            merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/collection_version> \"%s\" .\n" % (subject, item["version"]))
             skip = (subject in blacklist or label[1:] in blacklist)
             if skip:
                 merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/excluded_from_graph> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean> .\n" % subject)
-- 
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