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 <peter.amstutz@curii.com>
---
 bh20simplewebuploader/main.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

(limited to 'bh20simplewebuploader')

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 73503b4..405544c 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -675,13 +675,27 @@ sparqlURL='http://sparql.genenetwork.org/sparql/'
 @app.route('/resource/<id>')
 def resource(id):
     """Get a COVID19 resource using identifier"""
+
     query=f"""
 PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
 PREFIX sio: <http://semanticscience.org/resource/>
 select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequenceuri
+where {{
 {{
    ?sample sio:SIO_000115 "{id}" .
    ?sequenceuri pubseq:sample ?sample .
+}}
+union
+{{
+   <http://collections.lugli.arvadosapi.com/c={id}/sequence.fasta> pubseq:sample ?sample .
+   ?sequenceuri pubseq:sample ?sample .
+}}
+union
+{{
+   <http://covid19.genenetwork.org/resource/{id}> pubseq:sample ?sample .
+   ?sequenceuri pubseq:sample ?sample .
+}}
+
    ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
    ?geo rdfs:label ?geoname .
    ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
-- 
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