Merge pull request #83 from BonfaceKilz/feature/display-content-sequences

Feature/display fasta count on a map

7 files changed, 68 insertions, 31 deletions

diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css
index cadb9a5..5a9f231 100644
--- a/bh20simplewebuploader/static/main.css
+++ b/bh20simplewebuploader/static/main.css
@@ -47,6 +47,11 @@ h2 > svg {
     float: right;
 }
 
+#map {
+    width: 800px;
+    height: 440px;
+    border: 1px solid #AAA;
+}
 /* ---- start menu ---- */
 
 /* Add a black background color to the top navigation */
@@ -227,17 +232,6 @@ a {
     column-width: 250px;
 }
 
-pre code {
-    background-color: #eee;
-    display: flex;
-    width: max-content;
-    margin: 0 auto;
-    overflow-y: scroll;
-    max-height: 300px;
-    padding: 10px;
-    border: solid 1px black;
-}
-
 .record, .record .field-group, .record .field-group .field {
     display: flex;
     flex-direction: column;
@@ -261,12 +255,15 @@ pre code {
 .search-section {
     display: flex;
     justify-content: space-between;
+    width: max-content;
 }
 
+.filter-options {
+    width: 100%;
+}
 .search-section .filter-options {
     display: flex;
     flex-direction: column;
-    width: max-content;
     padding: 20px;
 }
 
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index efefe70..f2e5d99 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -13,15 +13,43 @@ function myFunction() {
     }
 }
 
+let map = L.map( 'map', {
+  center: [37.0902, -95.7129],  // Default to U.S.A
+  minZoom: 3,
+  zoom: 0
+});
+L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', {
+  attribution: '&copy; <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a>',
+  subdomains: ['a','b','c']
+}).addTo( map );
+
+let markers = L.markerClusterGroup().addTo(map)
+
+
 function fetchAPI(apiEndPoint) {
   fetch(scriptRoot + apiEndPoint)
     .then(response => {
       return response.json();
     })
     .then(data => {
-      document.getElementById("json").textContent = JSON.stringify(data, undefined, 2);
+      markers.clearLayers();
       document.getElementById("results").classList.remove("invisible");
       document.getElementById("loader").classList.add("invisible");
+      if (!(apiEndPoint === "/api/getAllaccessions")) {
+        for (let i = 0; i < data.length; i++) {
+          let {"Fasta Count": fastaCount, GPS, LocationLabel: label } = data[i];
+          let coordinates = GPS.match(/Point\((-?[0-9]+(?:.(?:[0-9]+)?)?) (-?[0-9]+(?:.(?:[0-9]+)?)?)\)/);
+          if (!(coordinates == null)) {
+            let lat, lon;
+            [lon, lat] = coordinates.slice(1, 3).map(parseFloat);
+            let point = L.point()
+            let marker = L.marker([lat, lon]);
+            marker.bindPopup("<b>" + label + "</b><br/>" + "FastaCount: " +fastaCount);
+            markers.addLayer(marker)
+          }}
+      }
+      // Reload the map
+      map.invalidateSize();
     });
   document.getElementById("results").classList.add("invisible");
   document.getElementById("loader").classList.remove("invisible");
diff --git a/bh20simplewebuploader/templates/demo-run.html b/bh20simplewebuploader/templates/demo-run.html
index a80281c..a8f9edc 100644
--- a/bh20simplewebuploader/templates/demo-run.html
+++ b/bh20simplewebuploader/templates/demo-run.html
@@ -13,15 +13,14 @@
 
   </div>
 
-  <div id="loader" class="loader invisible">
-  </div>
-
-  <section id="results" class="invisible">
-    <pre><code id="json"></code></pre>
-  </section>
-
+</section>
+<div id="loader" class="loader invisible">
+</div>
 
+<section id="results" class="invisible">
+    <div id="map"></div>
 </section>
+
  <section>
     <div id="table"></div>
-  </section>
+ </section>
diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html
index d9ebae2..76c19c4 100644
--- a/bh20simplewebuploader/templates/demo.html
+++ b/bh20simplewebuploader/templates/demo.html
@@ -6,9 +6,6 @@
     {% include 'menu.html' %}
     {% include 'search.html' %}
     {% include 'demo-run.html' %}
-
-    WIP
-
     {% include 'footer.html' %}
 
     <script type="text/javascript">
@@ -25,7 +22,6 @@
                   span.appendChild(txt);
               });
       });
-
     </script>
   </body>
 
diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html
index 0218278..9326b1e 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -1,5 +1,4 @@
 <br>
-</p>
 <section class="footer">
   <div class="about">
     <div>
@@ -40,4 +39,5 @@
       </small>
     </center>
   </div>
-</class>
+</section>
+<script type="text/javascript" src="/static/main.js"></script>
diff --git a/bh20simplewebuploader/templates/header.html b/bh20simplewebuploader/templates/header.html
index 5c0e1a0..0ac5157 100644
--- a/bh20simplewebuploader/templates/header.html
+++ b/bh20simplewebuploader/templates/header.html
@@ -3,8 +3,25 @@
         <link href="/static/main.css" rel="stylesheet" type="text/css">
         <meta name="viewport" content="width=device-width, initial-scale=1">
         <title>COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource</title>
-        <script type="text/javascript" src="/static/main.js"></script>
         {% if blog %}
         <link rel="Blog stylesheet" type="text/css" href="/static/blog.css" />
         {% endif %}
+        <link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css"
+              integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ=="
+              crossorigin=""/>
+        <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.css"
+              integrity="sha512-RLEjtaFGdC4iQMJDbMzim/dOvAu+8Qp9sw7QE4wIMYcg2goVoivzwgSZq9CsIxp4xKAZPKh5J2f2lOko2Ze6FQ=="
+              crossorigin=""/>
+
+        <link rel="stylesheet" href="https://unpkg.com/leaflet.markercluster@1.4.1/dist/MarkerCluster.Default.css"
+              integrity="sha512-BBToHPBStgMiw0lD4AtkRIZmdndhB6aQbXpX7omcrXeG2PauGBl2lzq2xUZTxaLxYz5IDHlmneCZ1IJ+P3kYtQ=="
+              crossorigin=""/>
+
+        <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js"
+                integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew=="
+                crossorigin=""></script>
+
+        <script src="https://unpkg.com/leaflet.markercluster@1.4.1/dist/leaflet.markercluster.js"
+                integrity="sha512-MQlyPV+ol2lp4KodaU/Xmrn+txc1TP15pOBF/2Sfre7MRsA/pB4Vy58bEqe9u7a7DczMLtU5wT8n7OblJepKbg=="
+                crossorigin=""></script>
     </head>
diff --git a/bh20simplewebuploader/templates/search.html b/bh20simplewebuploader/templates/search.html
index 1257ee2..dbdca90 100644
--- a/bh20simplewebuploader/templates/search.html
+++ b/bh20simplewebuploader/templates/search.html
@@ -1,10 +1,10 @@
 <div class="search">
-  <input id="search-input" id="global-search" type="search" placeholder="FASTA uri" required>
+  <input id="search-input" type="search" placeholder="FASTA uri" required>
   <button class="button search-button" type="submit" onclick="search()">
     <span class="icon ion-search">
       <span class="sr-only">Search</span>
     </span>
   </button>
-   <span class="dropt" title="http://collections.lugli.arvadosapi.com/c=00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta">(example)<span style="width:500px;"></span>
+  <span class="dropt" title="http://collections.lugli.arvadosapi.com/c=00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta">(example)<span style="width:500px;"></span></span>
 </div>
-</section>
+