Merge branch 'master' of github.com:pjotrp/bh20-seq-resource

3 files changed, 11 insertions, 15 deletions

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 865af97..1dff207 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -439,12 +439,15 @@ def getAllaccessions():
 @app.route('/api/getDetailsForSeq', methods=['GET'])
 def getDetailsForSeq():
     seq_id = request.args.get('seq')
-    query="""SELECT DISTINCT ?key ?value WHERE {<placeholder> ?x [?key ?value]}"""
+    query="""SELECT DISTINCT ?key ?key_label ?value WHERE {
+    <http://arvados.org/keep:00a6af865453564f6a59b3d2c81cc7c1+123/sequence.fasta> ?x [?key ?value] .
+    OPTIONAL {?key <http://www.w3.org/2000/01/rdf-schema#label> ?key_tmp_label } .
+    BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?key) as ?key_label)}"""
     query=query.replace("placeholder", seq_id)
     payload = {'query': query, 'format': 'json'}
     r = requests.get(baseURL, params=payload)
     result = r.json()['results']['bindings']
-    return jsonify([{'uri': x['key']['value'],
+    return jsonify([{'uri': x['key']['value'], 'key_label': x['key_label']['value'],
                      'value': x['value']['value']} for x in result])
 
 
@@ -463,18 +466,6 @@ def getSEQCountbytech():
                      'tech': x['tech']['value'],
                      'Label': x['tech_label']['value']} for x in result])
 
-## Is this one really necessary or should we just use getSEQCountbytech instead?
-@app.route('/api/getAvailableTech', methods=['GET'])
-def getAvailableTech():
-    query="""SELECT distinct ?tech ?tech_label WHERE
-    {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech]
-     BIND (concat(?tech,"_label") as ?tech_label)
-    } """
-    payload = {'query': query, 'format': 'json'}
-    r = requests.get(baseURL, params=payload)
-    result = r.json()['results']['bindings']
-    return str(result)
-
 ## List all Sequences/submissions by a given tech, as example e.g. http://purl.obolibrary.org/obo/OBI_0000759
 ## Has to be encoded again so should be --> http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000759
 @app.route('/api/getSEQbytech', methods=['GET'])
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index 37a7b72..7d7cef8 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -146,7 +146,7 @@
                                          {{ 'placeholder=http://www.wikidata.org/entity/Q30' if record['id']=='metadata.sample.collection_location'}}
                                          {{ 'placeholder=MyUniqueSampleId.1' if record['id']=='metadata.sample.sample_id'}}
                                          {{ 'value=http://purl.obolibrary.org/obo/NCBITaxon_2697049' if record['id']=='metadata.virus.virus_species'}}
-                                         {{ 'readonly=1 value=http://identifiers.org/insdc/MT334571.1#sequence' if record['id']=='metadata.id'}}
+                                         {{ 'readonly=1 value=http://genenetwork.org/submission' if record['id']=='metadata.id'}}
                                          name="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}"
                                          {{ "required" if record['required'] else "" }} {{ ("step=" + record['step']) if 'step' in record else ""}}>
                                 {% endif %}
diff --git a/paper/paper.md b/paper/paper.md
index 4df267f..cf9ba92 100644
--- a/paper/paper.md
+++ b/paper/paper.md
@@ -47,6 +47,9 @@ authors:
   - name: Andrea Guarracino
     orcid: https://orcid.org/0000-0001-9744-131X
     affiliation: 14
+  - name: Danielle Welter
+    orcid: https://orcid.org/0000-0003-1058-2668
+    affiliation: 15
 affiliations:
   - name: Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA.
     index: 1
@@ -62,6 +65,8 @@ affiliations:
     index: 8
   - name: Centre for Molecular Bioinformatics, Department of Biology, University Of Rome Tor Vergata, Rome, Italy
     index: 14
+  - name: Luxembourg Centre for Systems Biomedecine, University of Luxembourg, Luxembourg
+    index: 15
 date: 11 April 2020
 event: COVID2020
 group: Public Sequence Uploader