Merge branch 'master' into ebi-submit

9 files changed, 140 insertions, 119 deletions

diff --git a/bh20simplewebuploader/static/blog.css b/bh20simplewebuploader/static/blog.css
index 82a7c51..3ee8c44 100644
--- a/bh20simplewebuploader/static/blog.css
+++ b/bh20simplewebuploader/static/blog.css
@@ -4,12 +4,13 @@
 .timestamp { font-family: monospace; color: darkgreen; }
 
 h1,h2 { font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,monospace; color:black;background-color:#F0F8FF; }
-h2 { color: darkblue; }
-h3,h4 { color: black; }
+h2 { color: black; }
+h3,h4 { color: black; margin:0; }
 code { color: darkblue; }
-body {font-family: Palatino, 'Palatino Linotype', serif; color:black;background-color:#e5d8f0; font-size: large }
+body {font-family: Palatino, 'Palatino Linotype', serif; color:black; background-color:white; font-size: large }
 
-div.verbatim { margin: 30px; color: black; background-color: white; border-style:outset; font-family: palatino font, monospace; font-size:80%;  font-weight:bold; }
+div.verbatim { margin: 30px; color: black; background-color: white; border-style:outset;
+               font-family: palatino font, monospace; font-size:80%;  font-weight:bold; }
 div.quote { font-family: palatino font, monospace; font-size:80%; }
 div.quotation { font-family: palatino font, monospace; font-size:80%; }
 pre.example { margin: 30px; font-family: prestige, monospace; color:black; font-size:70%; background-color: lightyellow;  }
@@ -23,10 +24,10 @@ div[id="text-table-of-contents"]{
 }
 div[class^="outline-text"] {
     margin: 10px;
-    background-color:#ebe6f0;
-    border-style: dotted;
-    border-color: #98bf21;
-    border-width: 1px;
+    // background-color:white;
+    // border-style: dotted;
+    // border-color: #98bf21;
+    // border-width: 1px;
     font-family: Palatino, 'Palatino Linotype', serif; color:black; font-size: large
 }
 span[class="todo TESTING"] {
diff --git a/bh20simplewebuploader/static/image/CWL.png b/bh20simplewebuploader/static/image/CWL.png
new file mode 100644
index 0000000..81d1807
--- /dev/null
+++ b/bh20simplewebuploader/static/image/CWL.png
Binary files differdiff --git a/bh20simplewebuploader/static/image/ESR.png b/bh20simplewebuploader/static/image/ESR.png
new file mode 100644
index 0000000..557c798
--- /dev/null
+++ b/bh20simplewebuploader/static/image/ESR.png
Binary files differdiff --git a/bh20simplewebuploader/static/image/curii.logo.ai.png b/bh20simplewebuploader/static/image/curii.logo.ai.png
new file mode 100644
index 0000000..401afad
--- /dev/null
+++ b/bh20simplewebuploader/static/image/curii.logo.ai.png
Binary files differdiff --git a/bh20simplewebuploader/static/image/curii.logo.ai.svg b/bh20simplewebuploader/static/image/curii.logo.ai.svg
new file mode 100644
index 0000000..e87ea05
--- /dev/null
+++ b/bh20simplewebuploader/static/image/curii.logo.ai.svg
@@ -0,0 +1,3 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+<svg width="1333.3" height="1333.3" version="1.1" viewBox="0 0 1333.3 1333.3" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><metadata><rdf:RDF><cc:Work rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/><dc:title/></cc:Work></rdf:RDF></metadata><defs><clipPath id="clipPath18"><path d="m0 1e3h1e3v-1e3h-1e3z"/></clipPath></defs><g transform="matrix(1.3333 0 0 -1.3333 0 1333.3)"><g clip-path="url(#clipPath18)"><g transform="translate(473.7 553.52)"><path d="m0 0c-23.91 0-41.063-17.932-41.063-44.182 0-26.251 17.153-44.179 41.063-44.179 17.414 0 31.448 5.714 40.805 16.63l16.63-16.63c-12.476-16.377-32.488-25.735-58.734-25.735-41.063 0-69.653 28.329-69.653 69.914 0 41.843 28.59 70.428 69.653 70.428 24.95 0 44.439-8.053 57.174-22.611l-16.37-19.229c-9.619 9.876-22.875 15.851-39.505 15.594" fill="#008a82"/></g><g transform="translate(681.34 578.73)"><path d="m0 0v-138.26h-29.889v27.029c-9.355-19.232-26.765-27.806-49.377-28.07-31.707 0-50.676 20.276-50.676 53.281v86.022h29.884v-77.707c0-20.792 12.216-33.526 32.228-33.526 23.911 0.523 37.941 18.972 37.941 43.143v68.09z" fill="#008a82"/></g><g transform="translate(796.73 579.77)"><path d="m0 0v-28.585c-27.809 1.556-45.481-14.815-47.818-38.468v-72.248h-29.887v138.26h29.887v-27.546c9.356 18.71 25.99 28.585 47.818 28.585" fill="#008a82"/></g><g transform="translate(847.15 618.24)"><path d="m0 0c0-10.136-7.54-17.673-17.412-17.673-9.877 0-17.413 7.537-17.413 17.673 0 10.396 7.536 17.933 17.413 17.933 9.872 0 17.412-7.537 17.412-17.933" fill="#f15a29"/></g><path d="m844.54 440.47h-29.625v138.26h29.625z" fill="#008a82"/><g transform="translate(914.46 618.24)"><path d="m0 0c0-10.136-7.541-17.673-17.413-17.673-9.876 0-17.413 7.537-17.413 17.673 0 10.396 7.537 17.933 17.413 17.933 9.872 0 17.413-7.537 17.413-17.933" fill="#f15a29"/></g><path d="m911.85 440.47h-29.625v138.26h29.625z" fill="#008a82"/><g transform="translate(131.67 492.85)"><path d="m0 0c0.628 4.633 3.756 8.256 7.824 9.843l-9.454 65.551c-0.213 0.021-0.426-0.01-0.638 0.021-2.008 0.27-3.807 1.046-5.367 2.126l-57.718-52.611c2.31-21.875 9.31-42.198 19.929-60.052l46.065 29.321c-0.641 1.805-0.924 3.766-0.641 5.801" fill="#f15a29"/></g><g transform="translate(135.54 569.04)"><path d="m0 0 9.451-65.545c0.223-0.018 0.432 0.01 0.648-0.02 0.975-0.131 1.887-0.395 2.767-0.737l38.262 56.827-44.955 14.619c-1.414-2.373-3.608-4.149-6.173-5.144" fill="#f15a29"/></g><g transform="translate(280.25 609.22)"><path d="m0 0-48.729-0.574c-1.211-5.586-6.039-9.562-11.655-9.744l-24.468-36.342 53.617-17.44c0 0.809-0.074 1.62-0.051 2.43 0.912 25.152 12.634 47.22 31.286 61.67" fill="#f15a29"/></g><g transform="translate(217.14 623.42)"><path d="m0 0 2.255 58.382c-4.958 0.183-9.984 0.112-15.047-0.205-15.084-0.972-29.49-4.186-42.934-9.259l51.399-50.633c1.31 0.834 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1.522-29.071-4.033-57.766-26.257-78.143-2.545-2.344-5.248-4.393-8.036-6.28 72.262 13.991 124.59 79.812 119.73 155.21-0.078 1.306-0.227 2.592-0.345 3.888" fill="#008a82"/></g><g transform="translate(250.67 529.01)"><path d="m0 0c-8.863-1.971-17.477-5.104-25.76-9.947 7.733-9.046 15.469-18.091 23.188-27.143 4.901-5.729-4.405-12.76-9.275-7.059-7.844 9.184-15.692 18.355-23.533 27.543-3.244-2.674-6.116-5.496-8.563-8.494 13.566-16.281 27.111-32.576 40.666-48.876 4.826-5.793-4.486-12.83-9.286-7.061-12.67 15.225-25.348 30.468-38.019 45.701-2.14-4.209-3.767-8.604-4.84-13.168 8.495-9.946 16.998-19.892 25.493-29.843 4.898-5.729-4.411-12.758-9.281-7.061-6.019 7.032-12.026 14.071-18.048 21.114 0 0-4.766-16.237-0.865-52.291-1.66 0.746-3.085 2.109-3.847 4.189-9.88 27.309-16.654 62.017 0.85 88.074 12.678 18.854 32.288 30.459 53.735 36.456l-51.115 16.627-39.174-58.167c2.461-2.63 3.791-6.261 3.274-10.104-0.661-4.881-4.104-8.68-8.509-10.1l7.041-82.087c11.054-4.806 22.783-8.293 34.971-10.297 31.35 2.055 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\ No newline at end of file
diff --git a/bh20simplewebuploader/static/image/edit.png b/bh20simplewebuploader/static/image/edit.png
new file mode 100644
index 0000000..571b08c
--- /dev/null
+++ b/bh20simplewebuploader/static/image/edit.png
Binary files differdiff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css
index b9b27f4..6e651a4 100644
--- a/bh20simplewebuploader/static/main.css
+++ b/bh20simplewebuploader/static/main.css
@@ -47,7 +47,7 @@ h2 > svg {
     float: right;
 }
 
-#map {
+#mapid {
     width: 800px;
     height: 440px;
     border: 1px solid #AAA;
@@ -178,7 +178,7 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; }
 
 .about {
     display: grid;
-    grid-template-columns: repeat(2, 1fr);
+    grid-template-columns: 1fr 1fr;
     grid-auto-flow: row;
 }
 
@@ -229,7 +229,7 @@ a {
 #metadata_fill_form {
     column-count: 4;
     margin-top: 0.5em;
-    column-width: 250px;
+    column-width: 15em;
 }
 
 .record, .record .field-group, .record .field-group .field {
@@ -238,6 +238,8 @@ a {
     -webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */
     page-break-inside: avoid; /* Firefox */
     break-inside: avoid;
+    display: block;
+    width: 90%;
 }
 
 .record {
@@ -258,6 +260,10 @@ a {
     width: max-content;
 }
 
+.control {
+    width: 100%;
+}
+
 .filter-options {
     width: 100%;
 }
@@ -304,9 +310,10 @@ footer {
 }
 
 .sponsors img {
-    width: 80%;
-    display:block;
-    margin:auto;
+    width: auto;
+    display: block;
+    margin: auto;
+    height: 4em;
 }
 
 .loader {
@@ -377,3 +384,22 @@ div.status {
     vertical-align: top;
     border-bottom: 1px solid #ddd;
 }
+
+.map {
+    padding: 20px 32px;
+    // display: inline-block;
+}
+
+.editbutton {
+    float: right;
+    text-align: right;
+    background-color: lightgrey;
+    border: 2px solid #4CAF50;
+    border-radius: 12px;
+    color: black;
+    padding: 5px 32px;
+    // text-decoration: none;
+    display: inline-block;
+    font-size: 16px;
+    box-shadow: 0 8px 16px 0 rgba(0,0,0,0.2), 0 6px 20px 0 rgba(0,0,0,0.19);
+}
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 751e478..1633c25 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -13,70 +13,41 @@ 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 => {
-        console.log(data);
-      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 {"count": fastaCount, GPS, LocationLabel: label } = data[i];
-          let coordinates = GPS.split(" ");
-          if (!(coordinates == null)) {
-            let lat, lon;
-            [lon, lat] = coordinates.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");
-
-}
-
-// Copy from function above but now added as table instead of plain json
-function fetchAPIV2(apiEndPoint) {
-  fetch(scriptRoot + apiEndPoint)
-    .then(response => {
-      return response.json();
-    })
-    .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>"
-       }
-       htmlString=htmlString+"</table>"
-
-      document.getElementById("table").innerHTML = htmlString
-    });
-
-  document.getElementById("results").classList.add("invisible");
+    fetch(scriptRoot + apiEndPoint)
+        .then(response => {
+            return response.json();
+        })
+        .then(data => {
+            console.log(data);
+        });
+    document.getElementById("map_view").classList.add("invisible");
+    document.getElementById("loader").classList.remove("invisible");
+}
+
+// Copy from function above but now output HTML table instead of plain json
+function fetchHTMLTable(apiEndPoint) {
+    fetch(scriptRoot + apiEndPoint)
+        .then(response => {
+            return response.json();
+        })
+        .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++) {
+                htmlString=htmlString+"<tr><td>"+data[i]["label"]+"</td><td>"+data[i]["count"]+"<td></tr>"
+            }
+            htmlString=htmlString+"</table>"
+
+            document.getElementById("table").innerHTML = htmlString
+        });
 }
 
 
@@ -85,36 +56,39 @@ let search = () => {
   fetchAPI(scriptRoot + "/api/getDetailsForSeq?seq=" + encodeURIComponent(m));
 }
 
+// Get count from Arvados
 let fetchCount = () => {
   fetchAPI("/api/getCount");
 }
 
+// Get count from Virtuoso
 let fetchCountDB = () => {
   fetchAPI("/api/getCountDB");
 }
 
 let fetchSEQCountBySpecimen = () => {
-  fetchAPIV2("/api/getSEQCountbySpecimenSource");
+  fetchHTMLTable("/api/getSEQCountbySpecimenSource");
 }
 
 let fetchSEQCountByLocation = () => {
-  fetchAPIV2("/api/getSEQCountbyLocation");
+  fetchHTMLTable("/api/getSEQCountbyLocation");
 }
 
 let fetchSEQCountByTech = () => {
-  fetchAPIV2("/api/getSEQCountbytech");
+  fetchHTMLTable("/api/getSEQCountbytech");
 }
 
 let fetchAllaccessions = () => {
-  fetchAPI("/api/getAllaccessions");
+  fetchHTMLTable("/api/getAllaccessions");
 };
 
-let fetchCountByGPS = () => {
-  fetchAPI("/api/getCountByGPS");
+let fetchMap = () => {
+    fetchAPI("/api/getCountByGPS");
+    updateMapMarkers();
 };
 
 let fetchSEQCountbyLocation = () => {
-  fetchAPIV2("/api/getSEQCountbyLocation");
+  fetchHTMLTable("/api/getSEQCountbyLocation");
 };
 
 let fetchSEQByLocation = () => {
@@ -122,7 +96,7 @@ let fetchSEQByLocation = () => {
 };
 
 let fetchSEQCountbyContinent = () => {
-  fetchAPIV2("/api/getSEQCountbyContinent");
+  fetchHTMLTable("/api/getSEQCountbyContinent");
 }
 
 
@@ -195,7 +169,7 @@ function addField(e) {
   // Increment the number and use the keypath and number to set IDs and cross
   // references.
   // TODO: Heavily dependent on the form field HTML. Maybe we want custom
-  // elements for the labeled controlsd that know how to be list items?
+  // elements for the labeled controls that know how to be list items?
   fieldNumber++
   newField.dataset.number = fieldNumber
   let newID = keypath + '[' + fieldNumber + ']'
@@ -252,36 +226,3 @@ function on_submit_button() {
         return false;
     }
 }
-
-
-
-//
-
-function drawMap(){
-
-// initialize the map on the "map" div with a given center and zoom
-var mymap = L.map('mapid').setView([51.505, -0.09], 1);
-
-L.tileLayer('https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', {
-    attribution: '&copy; <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> contributors'
-}).addTo(mymap);
-
-fetch(scriptRoot + "api/getCountByGPS")
-    .then(response => {
-    console.log(response)
-      return response.json();
-    })
-    .then(data => {
-
-   for (var i=0; i<data.length;i++) {
-   gps=data[i]["GPS"].split(" ")
-    var circle = L.circle([gps[1], gps[0]], {
-    color: 'red',
-    fillColor: '#f03',
-    fillOpacity: 0.5,
-    radius: parseInt(data[i]["count"])  //not working for whatever reason
-        }).addTo(mymap);
-      }
-
-      });
-}
diff --git a/bh20simplewebuploader/static/map.js b/bh20simplewebuploader/static/map.js
new file mode 100644
index 0000000..1003f7d
--- /dev/null
+++ b/bh20simplewebuploader/static/map.js
@@ -0,0 +1,50 @@
+
+var map = L.map( 'mapid', {
+    center: [51.505, -0.09],  // Default to U.S.A
+    minZoom: 2,
+    zoom: 0
+});
+
+L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', {
+    attribution: '&copy; <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> | <a href="http://covid19.genenetwork.org/">COVID-19 PubSeq</a>',
+    subdomains: ['a','b','c']
+}).addTo(map);
+
+
+function drawMap(){
+    var mymap = map;
+
+    fetch(scriptRoot + "api/getCountByGPS")
+        .then(response => {
+            console.log(response)
+            return response.json();
+        })
+        .then(data => {
+            updateMapMarkers(data);
+
+      });
+    document.getElementById("map_view").classList.remove("invisible");
+    map.invalidateSize();
+}
+
+
+
+/* This function updates the map with markers
+ *
+*/
+function updateMapMarkers(data) {
+    let markers = L.markerClusterGroup();
+    for (let i = 0; i < data.length; i++) {
+        let {"count": fastaCount, GPS, LocationLabel: label } = data[i];
+        let coordinates = GPS.split(" ");
+        if (!(coordinates == null)) {
+            let lat, lon;
+            [lon, lat] = coordinates.map(parseFloat);
+            let point = L.point()
+            marker = (L.marker([lat, lon]));
+            marker.bindPopup("<b>" + label + "</b><br/>" + "SARS-CoV-2<br/>sequences: " +fastaCount);
+            markers.addLayer(marker);
+        }
+    }
+    map.addLayer(markers);
+}