From 5867eb6953e2e6564eb79d6f824952ce0bf2e28b Mon Sep 17 00:00:00 2001
From: lltommy
Date: Sat, 14 Nov 2020 18:51:42 +0100
Subject: SPARQL playground: additional examples

---
 bh20simplewebuploader/main.py             | 72 ++++++++++++++++++++++++++++++-
 bh20simplewebuploader/static/main.js      |  9 ++++
 bh20simplewebuploader/templates/demo.html | 12 ++++--
 3 files changed, 88 insertions(+), 5 deletions(-)

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 73787c2..ea4ec10 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -1261,7 +1261,7 @@ PREFIX wikiE: <http://www.wikidata.org/entity/>"""
         }
         ORDER BY ?seq"""
 
-    description = "Get all samples and their information (key, values) that were taken in New York (Q1384)!"
+    description = "Get all sequences and all sequence information (key, values) that were taken in New York (Q1384)!"
     payload = {'query': prefix + query, 'format': 'json'}
     r = requests.get(sparqlURL, params=payload)
     result = r.json()['results']['bindings']
@@ -1319,4 +1319,72 @@ Order by ?age
     return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}],
                [{'seq': x['seq']['value'],
                  'gender': x['gender']['value'],
-                 'age': x['age']['value']} for x in result])
\ No newline at end of file
+                 'age': x['age']['value']} for x in result])
+
+
+@app.route('/api/demoGetSeqIllumina', methods=['GET'])
+def demoGetSeqIllumina():
+    prefix = """PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX efo: <http://www.ebi.ac.uk/efo/>"""
+    ##TODO adjust OBI_0600047 to NCIT_C153598 once new schema is live
+    query="""SELECT DISTINCT ?seq WHERE {
+?seq ?technologySchema [obo:OBI_0600047 efo:EFO_0008635 ]
+}"""
+
+
+    description = "List all sequences that have as 'sample_sequencing_technology' (NCIT_C153598) Illumina iSeq 100 (EFO_0008635)"
+    payload = {'query': prefix + query, 'format': 'json'}
+    r = requests.get(sparqlURL, params=payload)
+    result = r.json()['results']['bindings']
+    return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}],
+               [{'seq': x['seq']['value']} for x in result])
+
+
+
+
+@app.route('/api/demoGetSeqWithStrain', methods=['GET'])
+def demoGetSeqWithStrain():
+    prefix = """PREFIX SIO: <http://semanticscience.org/resource/>"""
+    query="""SELECT DISTINCT  ?strain ?seq WHERE {
+?seq ?virusSchema [SIO:SIO_010055 ?strain] 
+}"""
+
+    description = "List all sequences with data in 'virus_strain'. Show the strain and the relevant identifer!"
+    payload = {'query': prefix + query, 'format': 'json'}
+    r = requests.get(sparqlURL, params=payload)
+    result = r.json()['results']['bindings']
+    return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}],
+               [{'strain': x['strain']['value'],
+                'seq': x['seq']['value']} for x in result])
+
+
+
+@app.route('/api/demoGetContinentSpecimentSeqCount', methods=['GET'])
+def demoGetContinentSpecimentSeqCount():
+    prefix = """PREFIX obo: <http://purl.obolibrary.org/obo/> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX wiki: <http://www.wikidata.org/prop/direct/>"""
+    query="""SELECT ?continent_label ?specimen_source_label (count(?seq) as ?seqCount)  WHERE
+    {
+        ?seq ?x [obo:OBI_0001479  ?specimen_source] .
+        ?seq ?y [ obo:GAZ_00000448 ?location] .
+        
+        ?location wiki:P17 ?country .
+        ?location wiki:P30 ?continent .
+
+        ?specimen_source rdfs:label ?specimen_source_label .
+        ?continent rdfs:label ?continent_label.
+    }
+
+    GROUP BY ?specimen_source ?specimen_source_label ?continent_label
+    ORDER BY ?continent_label DESC(?seqCount)"""
+
+    description = "Show a count of sequences by continent and specimen_source. For readability the labels for specimen_source and ?continent are retrieved."
+    payload = {'query': prefix + query, 'format': 'json'}
+    r = requests.get(sparqlURL, params=payload)
+    result = r.json()['results']['bindings']
+    return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}],
+               [{'continent_label': x['continent_label']['value'],
+                'specimen_source_label': x['specimen_source_label']['value'],
+                'seqCount': x['seqCount']['value']} for x in result])
+
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 1aa2582..aa1f06f 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -238,7 +238,16 @@ let demoGetSeqByAgeGender = () => {
     demofetchHTMLTable("/api/demoGetSeqByAgeGender")
 }
 
+let demoGetSeqIllumina = () => {
+    demofetchHTMLTable("/api/demoGetSeqIllumina")
+}
+let demoGetSeqWithStrain = () => {
+    demofetchHTMLTable("/api/demoGetSeqWithStrain")
+}
 
+let demoGetContinentSpecimentSeqCount = () => {
+    demofetchHTMLTable("/api/demoGetContinentSpecimentSeqCount")
+}
 
 ////****** SPARQL playground functions ***************////
 
diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html
index 742185b..dc6281d 100644
--- a/bh20simplewebuploader/templates/demo.html
+++ b/bh20simplewebuploader/templates/demo.html
@@ -21,17 +21,23 @@
     <section class="search-section">
       <div id="playgroundButtonBox" class="filter-options" action="#">
         <div>
-          <button class="button" onclick="demoFetchSEQCountByLocation()">Count by Location</button>
-          <button class="button" onclick="demoGetSEQCountbytech()">Count by Sequencer</button>
+          <button class="button" onclick="demoFetchSEQCountByLocation()">Count by location</button>
+          <button class="button" onclick="demoGetSEQCountbytech()">Count by sequencer</button>
+          <button class="button" onclick="demoGetSeqIllumina()">Sequences done with Illumina iSeq 100</button>
           <button class="button" onclick="demoFetchInstitutesPublications()">Get list of publications</button>
+          <button class="button" onclick="demoGetSeqWithStrain()">Sequences and their virus_strain</button>
           <button class="button" onclick="demoFetchSEQCountBySpecimen()">Count by Specimen source</button>
           <button class="button" onclick="demoGetSEQCountbytechContinent()">Sequence Technologies used by continent</button>
           <button class="button" onclick="demoGetAuthors()">Get authors</button>
           <button class="button" onclick="demoGetLocationGps()">Locations and their GPS</button>
-          <button class="button" onclick="demoGetSequencePerDate()">Show Sequences by collection date</button>
+          <button class="button" onclick="demoGetSequencePerDate()">Show sequences by collection date</button>
           <button class="button" onclick="demoGetSouthAmericaSeq()">List sequences from South America</button>
           <button class="button" onclick="demoGetSeqByAgeGender()">Get Sequence by age and gender</button>
           <button class="button" onclick="demoGetNYsamples()">Get all NY samples</button>
+          <button class="button" onclick="demoGetContinentSpecimentSeqCount()">Sequence count by continent/specimen_source</button>
+
+
+
 
           <!-- <button class="button" onclick="fetchAllaccessions()">Show All accessions</button>
           <button class="button" onclick="fetchSEQCountbyContinent()">Count by Continent</button>-->
-- 
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