List by country and added to map

4 files changed, 82 insertions, 16 deletions

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 92cea2e..0be9d9f 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -668,6 +668,7 @@ def contact_page():
 ##
 sparqlURL='http://sparql.genenetwork.org/sparql/'
 
+
 ##
 # Example http://covid19.genenetwork.org/resource/MT326090.1
 # Example http://host/resource/SRR11621868
@@ -716,6 +717,30 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ
         institute=sample['institute']['value']
     return render_template('permalink.html',id=id,menu='',uri=f"http://covid19.genenetwork.org/resource/{id}",sequenceuri=sequenceuri,locationuri=locationuri,location=location,date=date,source=source,sampletype=sampletype,institute=institute,collectionuri=collectionuri,metauri=metauri)
 
+# http://covid19.genenetwork.org/location?label=http://www.wikidata.org/entity/Q114
+# http://localhost:5067/location?label=http://www.wikidata.org/entity/Q114
+@app.route('/location', methods=['GET'])
+def location():
+    """Show country resource"""
+    loc = request.args.get('label')
+    logging.info(loc)
+    logging.info("^^^^^^^^^^^^^^^^^^^^^^^^^^^^")
+    query = f"""
+    PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+    PREFIX sio: <http://semanticscience.org/resource/>
+    select distinct ?name ?date where
+    {{
+      ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <{loc}> .
+      ?sample <http://semanticscience.org/resource/SIO_000115> ?name .
+      ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
+    }} order by ?name
+    """
+    payload = {'query': query, 'format': 'json'}
+    r = requests.get(sparqlURL, params=payload)
+    result = r.json()['results']['bindings']
+    logging.info(result)
+    return render_template('list.html',id=loc,menu='',h=['name','date'],l=result)
+
 ## Dynamic API functions starting here
 ## This is quick and dirty for now, just to get something out and demonstrate the queries
 ## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON
@@ -753,7 +778,12 @@ def getCountDB():
 
 @app.route('/api/getAllaccessions', methods=['GET'])
 def getAllaccessions():
-    query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ <http://edamontology.org/data_2091> ?value ]}"""
+    query="""
+    SELECT DISTINCT ?fasta ?value WHERE
+    {
+      ?fasta ?x[ <http://edamontology.org/data_2091> ?value ]
+    }
+    """
     payload = {'query': query, 'format': 'json'}
     r = requests.get(sparqlURL, params=payload)
     result = r.json()['results']['bindings']
@@ -780,11 +810,13 @@ def getDetailsForSeq():
 # Endpoint should provide all necessary information to draw a map (!)
 @app.route('/api/getCountByGPS', methods=['GET'])
 def getCountByGPS():
-    query="""SELECT DISTINCT ?location ?location_label ?GPS (count(?fasta) as ?fastaCount) WHERE {
-    ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] .
-    ?location <http://www.wikidata.org/prop/direct/P625> ?GPS .
-    OPTIONAL { ?location rdfs:label ?key_tmp_label }
-    BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?location_label)
+    query="""
+    SELECT DISTINCT ?location ?location_label ?GPS (count(?fasta) as ?fastaCount) WHERE
+    {
+      ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] .
+      ?location <http://www.wikidata.org/prop/direct/P625> ?GPS .
+      OPTIONAL { ?location rdfs:label ?key_tmp_label }
+      BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?location_label)
     }
     GROUP BY ?location ?location_label ?GPS
     """
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 6e63ed3..89bc603 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -66,13 +66,6 @@ function fetchHTMLTable(apiEndPoint) {
         .then(data => {
             console.log(data)
             htmlString="<table>"
-
-            // Depending on what we want to explore we'd have to call a different function ....? But how to Include that?
-            /*
-            for (var i=0; i<data.length;i++) {
-                htmlString=htmlString+"<tr><td><a href='#' onclick='fetchSEQByLocation(\""+data[i]["key"]+"\");'>"+data[i]["label"]+"</a></td><td>"+data[i]["count"]+"<td></tr>"
-            }
-            */
             for (var i=0; i<data.length;i++) {
                 let url = data[i]["key"];
                 let label = data[i]["label"];
@@ -97,7 +90,6 @@ function fetchHTMLTable(apiEndPoint) {
   }
 ]
 
-
  */
 let searchGlobal = (toHTML) => {
     let m =  document.getElementById('search-input').value;
diff --git a/bh20simplewebuploader/static/map.js b/bh20simplewebuploader/static/map.js
index cabb63d..c01659f 100644
--- a/bh20simplewebuploader/static/map.js
+++ b/bh20simplewebuploader/static/map.js
@@ -86,7 +86,7 @@ function buildMapMarkers(data) {
             }}});
     // ---- Build the marker list
     for (let i = 0; i < data.length; i++) {
-        let {"count": fastaCount, GPS, LocationLabel: label } = data[i];
+        let {"count": fastaCount, GPS, Location: location, LocationLabel: label } = data[i];
         let countSeq = Number(fastaCount);
 
         let coordinates = GPS.split(" ");
@@ -95,7 +95,7 @@ function buildMapMarkers(data) {
             [lon, lat] = coordinates.map(parseFloat);
             let point = L.point()
             marker = new seqMarker([lat, lon],markerOptions={title: fastaCount+" sequences",sequences: countSeq});
-            marker.bindPopup("<b>" + label + "</b><br/>" + "SARS-CoV-2<br/>sequences: " +fastaCount);
+            marker.bindPopup("<b>" + label + "</b><br/>" + "SARS-CoV-2<br/><a href=\"/location?label="+location+"\">sequences: " +fastaCount + "</a>");
             markers.addLayer(marker);
         }
     }
diff --git a/bh20simplewebuploader/templates/list.html b/bh20simplewebuploader/templates/list.html
new file mode 100644
index 0000000..d50a045
--- /dev/null
+++ b/bh20simplewebuploader/templates/list.html
@@ -0,0 +1,42 @@
+<!DOCTYPE html>
+<html>
+  {% include 'header.html' %}
+  <body>
+    {% include 'banner.html' %}
+    {% include 'menu.html' %}
+
+    <hr>
+
+    <h1>{{id}}</h1>
+
+    <div class="content">
+    <section class="blog-entries">
+      <div class="blog-table">
+        {% for row in l: %}
+        <div class="blog-table-body">
+          <div class="blog-table-row">
+            {% for col in h: %}
+            <div class="blog-table-cell">
+              {% if col == 'name': %}
+                <a href="/resource/{{row[col]['value']}}">{{ row[col]['value'] }}</a>
+              {% else %}
+                {{ row[col]['value'] }}
+              {% endif %}
+            </div>
+            {% endfor %}
+          </div>
+        </div>
+        {% endfor %}
+      </div>
+    </section>
+
+    </div>
+
+    {% include 'footer.html' %}
+
+    <script type="text/javascript">
+      let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
+    </script>
+  </body>
+
+</html>