From 1082b907d816f5da52aba6233073737632d0242f Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 9 Nov 2020 17:20:27 -0500 Subject: Make resource link work for both portable data hashes and sample id Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/collect-seqs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'workflows') diff --git a/workflows/pangenome-generate/collect-seqs.py b/workflows/pangenome-generate/collect-seqs.py index af4a0dc..1a0807c 100644 --- a/workflows/pangenome-generate/collect-seqs.py +++ b/workflows/pangenome-generate/collect-seqs.py @@ -38,7 +38,7 @@ for item in validated: pdh = item["portable_data_hash"] with arvados.collection.CollectionReader(pdh, api_client=api, keep_client=keepclient) as col: with col.open("sequence.fasta", "rt") as fa: - subject = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % pdh + subject = "http://covid19.genenetwork.org/resource/%s" % pdh label = fa.readline().strip() merged_metadata.write("<%s> \"%s\" .\n" % (subject, label[1:].replace('"', '\\"'))) skip = (subject in blacklist or label[1:] in blacklist) -- cgit v1.2.3