aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorPeter Amstutz2020-11-10 11:54:10 -0500
committerGitHub2020-11-10 11:54:10 -0500
commit992c52f490024ffa34ac6c37c2e9434d34349340 (patch)
tree39e06404e04f1ac4ea0db3d368c029c2c55ee357
parentd213801678926e16135299a2e3ca0392a821507b (diff)
parentc01188ec20936462357b317f81567aadc64c8f33 (diff)
downloadbh20-seq-resource-992c52f490024ffa34ac6c37c2e9434d34349340.tar.gz
bh20-seq-resource-992c52f490024ffa34ac6c37c2e9434d34349340.tar.lz
bh20-seq-resource-992c52f490024ffa34ac6c37c2e9434d34349340.zip
Merge pull request #116 from arvados/uuid-for-resource
Use arvados uuids for RDF subjects.
-rw-r--r--bh20simplewebuploader/main.py5
-rw-r--r--workflows/pangenome-generate/collect-seqs.py5
2 files changed, 9 insertions, 1 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index fc145e6..1d7154c 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -707,6 +707,11 @@ 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)