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-rw-r--r--bh20simplewebuploader/templates/blog.html8
-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.html8
-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
13 files changed, 111 insertions, 96 deletions
diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html
index 823f8a1..f4c2a85 100644
--- a/bh20simplewebuploader/templates/blog.html
+++ b/bh20simplewebuploader/templates/blog.html
@@ -63,6 +63,14 @@
We explore the Arvados command line and API
</div>
</div>
+ <div class="blog-table-row">
+ <div class="blog-table-cell">
+ <a href="/blog?id=using-covid-19-pubseq-part6">Prepare for uploading to EBI/ENA</a>
+ </div>
+ <div class="blog-table-cell">
+ Generate the files needed for uploading to EBI/ENA
+ </div>
+ </div>
</div>
</div>
</section>
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 37a6b64..f84cef5 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -21,12 +21,15 @@
<img src="static/image/covid19biohackathon.png"></a>
</div>
<div class="sponsorimg">
- <a href="https://www.commonwl.org/"><img src="static/image/CWL.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">
@@ -44,6 +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 v1.2.3 (git 2.45.2) at 2024-11-22 20:03:12 +0000