Adding an additional example to the SPARQL playground

3 files changed, 80 insertions, 41 deletions

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 27dcd4b..87ef212 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -1066,7 +1066,7 @@ def getSEQbyLocationAndSpecimenSource():
     return str(result)
 
 
-################## SPARQL PLAYGORUND API function ################
+########################## SPARQL PLAYGORUND API function ####################
 
 @app.route('/api/demoGetSEQCountbySpecimenSource', methods=['GET'])
 def demoGetSEQCountbySpecimenSource():
@@ -1193,7 +1193,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>"""
 
 
 @app.route('/api/demoGetSEQCountbytech', methods=['GET'])
-def dempGetSEQCountbytech():
+def demoGetSEQCountbytech():
     prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>"""
 
@@ -1221,7 +1221,7 @@ def demoGetSequencePerDate():
     FILTER ( xsd:date(?date) < xsd:date("2020-03-01") )
     }
     ORDER BY ?date"""
-    description = "Show all sequences with a submission date before 2020-03-01! To accomplish this a FILTER expression is used. Since date is a string, we cast xsd:date(...)"
+    description = "Show all sequences with a collection date before 2020-03-01! To accomplish this a FILTER expression is used. Since date is a string, we cast xsd:date(...)"
     payload = {'query': prefix + query, 'format': 'json'}
     r = requests.get(sparqlURL, params=payload)
     result = r.json()['results']['bindings']
@@ -1229,8 +1229,8 @@ def demoGetSequencePerDate():
                    [{'seq': x['seq']['value'],
                      'date': x['date']['value']} for x in result])
 
-@app.route('/api/demoLocationGps', methods=['GET'])
-def demoLocationGps():
+@app.route('/api/demoGetLocationGps', methods=['GET'])
+def demoGetLocationGps():
     prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX wiki: <http://www.wikidata.org/prop/direct/>"""
 
@@ -1247,8 +1247,8 @@ PREFIX wiki: <http://www.wikidata.org/prop/direct/>"""
                    [{'location': x['location']['value'],
                      'GPS': x['GPS']['value']} for x in result])
 
-@app.route('/api/getNYsamples', methods=['GET'])
-def getNYsamples():
+@app.route('/api/demoGetNYsamples', methods=['GET'])
+def demoGetNYsamples():
     prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX wikiE: <http://www.wikidata.org/entity/>"""
 
@@ -1270,4 +1270,31 @@ PREFIX wikiE: <http://www.wikidata.org/entity/>"""
                      'key_label': x['key_label']['value'],
                      'key': x['key']['value'],
                      'value_label': x['value_label']['value'],
-                     'value': x['value']['value']} for x in result])
\ No newline at end of file
+                     'value': x['value']['value']} for x in result])
+
+
+@app.route('/api/demoGetSouthAmericaSeq', methods=['GET'])
+def demoGetSouthAmericaSeq():
+    prefix = """PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX wiki: <http://www.wikidata.org/prop/direct/> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+"""
+
+    query = """SELECT DISTINCT ?country_label ?seq WHERE
+    {
+      ?seq ?y [ obo:GAZ_00000448 ?location] .
+      ?location wiki:P17 ?country .
+      ?country rdfs:label ?country_label .
+      ?country wiki:P30 <http://www.wikidata.org/entity/Q18> .
+    }   
+ORDER BY ?country_label
+"""
+
+    description = "Show all sequences that are on the continent (P30) South America (Q18)! List the sequence identifiers and the country they belong too."
+    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'],
+                     'country_label': x['country_label']['value']} for x in result])
+
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 0e642c1..da196cf 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -164,29 +164,52 @@ let fetchCountDB = () => {
   fetchAPI("/api/getCountDB");
 }
 
+//////  old API functions, some might no be used //
+let fetchSEQCountByTech = () => {
+  fetchHTMLTable("/api/getSEQCountbytech");
+}
+
+let fetchAllaccessions = () => {
+  fetchHTMLTable("/api/getAllaccessions");
+};
+
+let fetchMap = () => {
+    fetchAPI("/api/getCountByGPS");
+    updateMapMarkers();
+};
+
+let fetchSEQByLocation = () => {
+  console.log("Missing - set parameter for request, retrieve data")
+};
+
+let fetchSEQCountbyContinent = () => {
+  fetchHTMLTable("/api/getSEQCountbyContinent");
+}
+/////////////////////////////////// End "old" function
+
 
-//****** SPARQL playground functions // keep old functionality as comments for now, might be transfered elsewhere
-let fetchSEQCountBySpecimen = (toHTML) => {
+////****** SPARQL playground functions ***************////
+let demoFetchSEQCountBySpecimen = (toHTML) => {
   //fetchHTMLTable("/api/getSEQCountbySpecimenSource");
   demofetchHTMLTable("/api/demoGetSEQCountbySpecimenSource")
 }
 
-let fetchSEQCountByLocation = () => {
+let demoFetchSEQCountByLocation = () => {
   //fetchHTMLTable("/api/getSEQCountbyLocation");
   demofetchHTMLTable("/api/demoGetSEQCountbyLocation")
 }
 
 //Get authors and there country/contitent where they come from
-let fetchAuthors = () => {
+let demoGetAuthors = () => {
     demofetchHTMLTable("/api/demoGetAuthors")
 }
 
 // Fetch all institutes/originating labs and their associeted publications
-let fetchInstitutesPublications = () => {
+let demoFetchInstitutesPublications = () => {
     demofetchHTMLTable("/api/demoInstitutesPublications")
 }
 
-//Fetch seqeenctechnologies used by continent
+// Fetch sequence technology used by continent
 let demoGetSEQCountbytechContinent = () => {
     demofetchHTMLTable("/api/demoGetSEQCountbytechContinent")
 }
@@ -199,35 +222,22 @@ let demoGetSequencePerDate = () => {
     demofetchHTMLTable('/api/demoGetSequencePerDate')
 }
 
-let demoLocationGps = () => {
-    demofetchHTMLTable("/api/demoLocationGps")
+let demoGetLocationGps = () => {
+    demofetchHTMLTable("/api/demoGetLocationGps")
 }
 
-let getNYsamples = () => {
-    demofetchHTMLTable("/api/getNYsamples")
+let demoGetNYsamples = () => {
+    demofetchHTMLTable("/api/demoGetNYsamples")
 }
 
-//old/unused functions
-let fetchSEQCountByTech = () => {
-  fetchHTMLTable("/api/getSEQCountbytech");
+let demoGetSouthAmericaSeq = () => {
+    demofetchHTMLTable("/api/demoGetSouthAmericaSeq")
 }
 
-let fetchAllaccessions = () => {
-  fetchHTMLTable("/api/getAllaccessions");
-};
 
-let fetchMap = () => {
-    fetchAPI("/api/getCountByGPS");
-    updateMapMarkers();
-};
 
-let fetchSEQByLocation = () => {
-  console.log("Missing - set parameter for request, retrieve data")
-};
 
-let fetchSEQCountbyContinent = () => {
-  fetchHTMLTable("/api/getSEQCountbyContinent");
-}
+////****** SPARQL playground functions ***************////
 
 
 /*
diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html
index ffebc91..393548c 100644
--- a/bh20simplewebuploader/templates/demo.html
+++ b/bh20simplewebuploader/templates/demo.html
@@ -21,17 +21,19 @@
     <section class="search-section">
       <div class="filter-options" action="#">
         <div>
-          <button class="button" onclick="fetchSEQCountByLocation()">Count by Location</button>
+          <button class="button" onclick="demoFetchSEQCountByLocation()">Count by Location</button>
           <button class="button" onclick="demoGetSEQCountbytech()">Count by Sequencer</button>
-          <button class="button" onclick="fetchInstitutesPublications()">Get list of publications</button>
-          <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button>
+          <button class="button" onclick="demoFetchInstitutesPublications()">Get list of publications</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="getNYsamples()">Get all NY samples</button>
-          <button class="button" onclick="fetchAuthors()">Get authors</button>
-          <button class="button" onclick="demoGetSequencePerDate()">Show Sequences before submission date</button>
-          <button class="button" onclick="demoLocationGps()">Locations and their GPS</button>
+          <button class="button" onclick="demoGetNYsamples()">Get all NY samples</button>
+          <button class="button" onclick="demoGetAuthors()">Get authors</button>
+          <button class="button" onclick="demoGetSequencePerDate()">Show Sequences by collection date</button>
+          <button class="button" onclick="demoGetLocationGps()">Locations and their GPS</button>
 
 
+          <button class="button" onclick="demoGetSouthAmericaSeq()">List sequences from South America</button>
+
 
 
           <!-- <button class="button" onclick="fetchAllaccessions()">Show All accessions</button>