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authorPjotr Prins2020-07-17 11:08:15 +0100
committerPjotr Prins2020-07-17 11:08:15 +0100
commit16bb5df907c79cd0ce6bea0015821a2ce51fb992 (patch)
treeddb9677cddcc463bb514300189cbd4300b9117ed /bh20simplewebuploader/templates
parent0be9983ef88fd3b925d8fa53e7f9ab2a28703bc0 (diff)
parentc69046ee9a5e24eadcd8cb885633328b0fd88011 (diff)
downloadbh20-seq-resource-16bb5df907c79cd0ce6bea0015821a2ce51fb992.tar.gz
bh20-seq-resource-16bb5df907c79cd0ce6bea0015821a2ce51fb992.tar.lz
bh20-seq-resource-16bb5df907c79cd0ce6bea0015821a2ce51fb992.zip
Merge branch 'master' into ebi-submit
Diffstat (limited to 'bh20simplewebuploader/templates')
-rw-r--r--bh20simplewebuploader/templates/blog.html4


-rw-r--r--bh20simplewebuploader/templates/blurb.html2


-rw-r--r--bh20simplewebuploader/templates/demo-run.html26


-rw-r--r--bh20simplewebuploader/templates/demo.html49


-rw-r--r--bh20simplewebuploader/templates/error.html2


-rw-r--r--bh20simplewebuploader/templates/footer.html12


-rw-r--r--bh20simplewebuploader/templates/header.html18


-rw-r--r--bh20simplewebuploader/templates/home.html15


-rw-r--r--bh20simplewebuploader/templates/map.html33


-rw-r--r--bh20simplewebuploader/templates/mapheader.html16


-rw-r--r--bh20simplewebuploader/templates/search.html10


-rw-r--r--bh20simplewebuploader/templates/status.html3


-rw-r--r--bh20simplewebuploader/templates/success.html2


-rw-r--r--bh20simplewebuploader/templates/validated.html17


14 files changed, 109 insertions, 100 deletions
diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html
index dbc0b99..823f8a1 100644
--- a/bh20simplewebuploader/templates/blog.html
+++ b/bh20simplewebuploader/templates/blog.html
@@ -9,9 +9,7 @@
     {{ embed|safe }}
     <hr>
 
-    <p>
-      Other blog entries:
-    </p>
+    <h1>Other blog entries</h1>
 
     {% else %}
     {% include 'blurb.html' %}
diff --git a/bh20simplewebuploader/templates/blurb.html b/bh20simplewebuploader/templates/blurb.html
index 80fd384..9eef7c2 100644
--- a/bh20simplewebuploader/templates/blurb.html
+++ b/bh20simplewebuploader/templates/blurb.html
@@ -2,7 +2,7 @@
   This is the COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
   SARS-CoV-2 virus sequences. COVID-19 PubSeq is a repository for
   sequences with a low barrier to entry for uploading sequence data
-  using best practices. I.e., data published with a creative commons
+  using best practices, including <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR data</a>. I.e., data published with a creative commons
   CC0 or CC-4.0 license with metadata using state-of-the art standards
   and, perhaps most importantly, providing standardised workflows that
   get triggered on upload, so that results are immediately available
diff --git a/bh20simplewebuploader/templates/demo-run.html b/bh20simplewebuploader/templates/demo-run.html
deleted file mode 100644
index a8f9edc..0000000
--- a/bh20simplewebuploader/templates/demo-run.html
+++ /dev/null
@@ -1,26 +0,0 @@
-<section class="search-section">
-  <div class="filter-options" action="#">
-    <p>[Demo] Display content sequences by: </p>
-    <div>
-      <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button>
-      <button class="button" onclick="fetchSEQCountByLocation()">Count by Location</button>
-      <button class="button" onclick="fetchSEQCountByTech()">Count by Sequencer</button>
-      <button class="button" onclick="fetchAllaccessions()">Show All accessions</button>
-      <button class="button" onclick="fetchSEQCountbyContinent()">Count by Continent</button>
-      <button class="button" onclick="fetchCountByGPS()">Map</button>
-
-    </div>
-
-  </div>
-
-</section>
-<div id="loader" class="loader invisible">
-</div>
-
-<section id="results" class="invisible">
-    <div id="map"></div>
-</section>
-
- <section>
-    <div id="table"></div>
- </section>
diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html
index 44aded0..75bc0e2 100644
--- a/bh20simplewebuploader/templates/demo.html
+++ b/bh20simplewebuploader/templates/demo.html
@@ -1,13 +1,51 @@
 <!DOCTYPE html>
 <html>
   {% include 'header.html' %}
+  {% include 'mapheader.html' %}
   <body>
     {% include 'banner.html' %}
     {% include 'menu.html' %}
-    {% include 'search.html' %}
-      <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences!</p>
-    {% include 'demo-run.html' %}
-    {% include 'footer.html' %}
+
+    <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences!</p>
+
+    <!--
+    <div class="search">
+      <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>
+    </div>
+    -->
+
+    <section class="search-section">
+      <div class="filter-options" action="#">
+        <p>[Demo] Display content sequences by: </p>
+        <div>
+          <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button>
+          <button class="button" onclick="fetchSEQCountByLocation()">Count by Location</button>
+          <button class="button" onclick="fetchSEQCountByTech()">Count by Sequencer</button>
+          <!-- <button class="button" onclick="fetchAllaccessions()">Show All accessions</button> -->
+          <button class="button" onclick="fetchSEQCountbyContinent()">Count by Continent</button>
+        </div>
+
+      </div>
+
+    </section>
+    <div id="loader" class="loader invisible">
+    </div>
+
+    <section id="map_view" class="map">
+      <div id="mapid"></div>
+    </section>
+
+    <section>
+      <div id="table"></div>
+    </section>
+
+ {% include 'footer.html' %}
 
     <script type="text/javascript">
       let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
@@ -24,7 +62,10 @@
               });
       });
 
+     drawMap()
+
     </script>
+
   </body>
 
 </html>
diff --git a/bh20simplewebuploader/templates/error.html b/bh20simplewebuploader/templates/error.html
index b1d9402..fc08aed 100644
--- a/bh20simplewebuploader/templates/error.html
+++ b/bh20simplewebuploader/templates/error.html
@@ -15,7 +15,7 @@
           </pre>
         </p>
         <p>
-            <a href="/">Click here to try again.</a>
+            <a href="/upload">Click here to try again.</a>
         </p>
         <hr>
     </body>
diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html
index a1dd4fd..f84cef5 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -21,14 +21,21 @@
           <img src="static/image/covid19biohackathon.png"></a>
       </div>
       <div class="sponsorimg">
-        <a href="https://www.commonwl.org/"><img src="static/image/CWL-Logo-Header.png"></a>
+        <a href="https://www.curii.com/"><img src="static/image/curii.logo.ai.png"></a>
       </div>
       <div class="sponsorimg">
         <a href="https://arvados.org/"><img src="static/image/arvados-logo.png"></a>
       </div>
       <div class="sponsorimg">
+        <a href="https://www.commonwl.org/"><img src="static/image/CWL.png"></a>
+      </div>
+      <div class="sponsorimg">
         <a href="https://uthsc.edu/"><img src="static/image/UTHSC-primary-stacked-logo-4c.png"></a>
       </div>
+      <div class="sponsorimg">
+        <a href="https://www.esr.cri.nz/"><img src="static/image/ESR.png"></a>
+      </div>
+
     </div>
   </div>
   <div class="footer">
@@ -40,6 +47,9 @@
     </center>
   </div>
 </section>
+{% if load_map %}
+<script type="text/javascript" src="/static/map.js"></script>
+{% endif %}
 <script type="text/javascript" src="/static/main.js"></script>
 
 <script type="text/javascript">
diff --git a/bh20simplewebuploader/templates/header.html b/bh20simplewebuploader/templates/header.html
index 0ac5157..1d66590 100644
--- a/bh20simplewebuploader/templates/header.html
+++ b/bh20simplewebuploader/templates/header.html
@@ -6,22 +6,4 @@
         {% 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/home.html b/bh20simplewebuploader/templates/home.html
index b90a18d..bede611 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -1,6 +1,7 @@
 <!DOCTYPE html>
 <html>
   {% include 'header.html' %}
+  {% include 'mapheader.html' %}
     <body>
       {% include 'banner.html' %}
       {% include 'menu.html' %}
@@ -44,7 +45,19 @@
                 </div>
         </section>
 
-{% include 'footer.html' %}
+      <section id="map_view" class="map">
+        <div id="mapid"></div>
+      </section>
+
+      {% include 'footer.html' %}
+
+
+      <script type="text/javascript">
+        let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
+
+        drawMap()
+
+      </script>
 
    </body>
 </html>
diff --git a/bh20simplewebuploader/templates/map.html b/bh20simplewebuploader/templates/map.html
deleted file mode 100644
index 595af0c..0000000
--- a/bh20simplewebuploader/templates/map.html
+++ /dev/null
@@ -1,33 +0,0 @@
-<!DOCTYPE html>
-<html>
-  {% include 'header.html' %}
-<link rel="stylesheet" href="https://unpkg.com/leaflet@1.6.0/dist/leaflet.css"
-   integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ=="
-   crossorigin=""/>
-
-    {% include 'banner.html' %}
-    {% include 'menu.html' %}
-    <div id="mapid" style="height: 500px;"></div>
-
-    {% include 'footer.html' %}
-
-
-
-
-       <script type="text/javascript">
-        let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
-      </script>
-
-<!-- Make sure you put this AFTER Leaflet's CSS -->
- <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js"
-   integrity="sha512-gZwIG9x3wUXg2hdXF6+rVkLF/0Vi9U8D2Ntg4Ga5I5BZpVkVxlJWbSQtXPSiUTtC0TjtGOmxa1AJPuV0CPthew=="
-   crossorigin=""></script>
-
-  <script>
-     //drawMap
-     drawMap()
-  </script>
-
-  </body>
-
-</html>
diff --git a/bh20simplewebuploader/templates/mapheader.html b/bh20simplewebuploader/templates/mapheader.html
new file mode 100644
index 0000000..ca62051
--- /dev/null
+++ b/bh20simplewebuploader/templates/mapheader.html
@@ -0,0 +1,16 @@
+  <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>
diff --git a/bh20simplewebuploader/templates/search.html b/bh20simplewebuploader/templates/search.html
index dbdca90..e69de29 100644
--- a/bh20simplewebuploader/templates/search.html
+++ b/bh20simplewebuploader/templates/search.html
@@ -1,10 +0,0 @@
-<div class="search">
-  <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>
-</div>
-
diff --git a/bh20simplewebuploader/templates/status.html b/bh20simplewebuploader/templates/status.html
index a1cf28f..e89437e 100644
--- a/bh20simplewebuploader/templates/status.html
+++ b/bh20simplewebuploader/templates/status.html
@@ -7,7 +7,8 @@
 
       <h1>Sequence upload processing status</h1>
 
-        <div class="status">
+      <div class="status">
+
 	  {{ table }}
         </div>
 
diff --git a/bh20simplewebuploader/templates/success.html b/bh20simplewebuploader/templates/success.html
index 9f0987c..c2302fa 100644
--- a/bh20simplewebuploader/templates/success.html
+++ b/bh20simplewebuploader/templates/success.html
@@ -9,7 +9,7 @@
         <h1>Upload Successful</h1>
         <hr>
         <p>
-            Your files have been uploaded. They should soon appear as output of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>.
+            Your files have been uploaded. You can track their <a href="/status">QC status</a>, once validated they will be part of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>.
         </p>
         <p>
             The upload log was:
diff --git a/bh20simplewebuploader/templates/validated.html b/bh20simplewebuploader/templates/validated.html
new file mode 100644
index 0000000..cee94bd
--- /dev/null
+++ b/bh20simplewebuploader/templates/validated.html
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html>
+  {% include 'header.html' %}
+    <body>
+      {% include 'banner.html' %}
+      {% include 'menu.html' %}
+
+      <h1>Validated sequences</h1>
+
+        <div class="status">
+	  {{ table }}
+        </div>
+
+{% include 'footer.html' %}
+
+   </body>
+</html>

 

generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-08-06 22:46:30 +0000