diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 5 | ||||
| -rw-r--r-- | workflows/pangenome-generate/collect-seqs.py | 5 |
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) |