Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

7 files changed, 110 insertions, 16 deletions

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 73503b4..1d7154c 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -7,6 +7,7 @@ import logging
 import os
 import sys
 import re
+import redis
 import string
 import ruamel.yaml as yaml
 import pkg_resources
@@ -252,8 +253,19 @@ def send_home():
     """
     Send the front page.
     """
-
-    return render_template('home.html', menu='HOME', load_map=True)
+    redis_client = redis.Redis(host=os.environ.get('HOST', 'localhost'),
+                               port=os.environ.get('PORT', 6379),
+                               db=os.environ.get('REDIS_DB', 0))
+    tweets = []
+    for tweet_id in redis_client.zrevrange('bh20-tweet-score:',
+                                           0, -1):
+        tweets.append(
+            {k.decode("utf-8"): v.decode("utf-8") for k, v in
+             redis_client.hgetall(tweet_id).items()}
+        )
+    return render_template('home.html', menu='HOME',
+                           tweets=tweets,
+                           load_map=True)
 
 
 @app.route('/upload')
@@ -675,13 +687,32 @@ sparqlURL='http://sparql.genenetwork.org/sparql/'
 @app.route('/resource/<id>')
 def resource(id):
     """Get a COVID19 resource using identifier"""
+
     query=f"""
 PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
 PREFIX sio: <http://semanticscience.org/resource/>
 select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequenceuri
+where {{
 {{
    ?sample sio:SIO_000115 "{id}" .
    ?sequenceuri pubseq:sample ?sample .
+}}
+union
+{{
+   <http://collections.lugli.arvadosapi.com/c={id}/sequence.fasta> pubseq:sample ?sample .
+   ?sequenceuri pubseq:sample ?sample .
+}}
+union
+{{
+   <http://covid19.genenetwork.org/resource/{id}> pubseq:sample ?sample .
+   ?sequenceuri pubseq:sample ?sample .
+}}
+union
+{{
+   ?sequenceuri <http://biohackathon.org/bh20-seq-schema/collection_pdh> "{id}" .
+   ?sequenceuri pubseq:sample ?sample .
+}}
+
    ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
    ?geo rdfs:label ?geoname .
    ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
@@ -699,8 +730,9 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ
     logging.info("^^^^^^^^^^^^^^^^^^^^^^^^^^^^")
     # return jsonify({'sequences': int(result[0]["num"]["value"])})
     sequenceuri=sample['sequenceuri']['value']
-    collectionuri=sequenceuri.split('sequence.fasta')[0]
-    metauri=collectionuri+'metadata.yaml'
+    m = re.match(r"http://collections.lugli.arvadosapi.com/c=([^/]*)/sequence.fasta|http://covid19.genenetwork.org/resource/(.*)", sequenceuri)
+    fastauri = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % m.group(1)
+    metauri = "http://collections.lugli.arvadosapi.com/c=%s/metadata.yaml" % m.group(1)
     locationuri=sample['geo']['value']
     location=sample['geoname']['value']
     date=sample['date']['value']
@@ -715,7 +747,18 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ
     institute=''
     if 'institute' in sample:
         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)
+    return render_template('permalink.html',
+                           id=id,
+                           menu='',
+                           uri=f"http://covid19.genenetwork.org/resource/{id}",
+                           sequenceuri=fastauri,
+                           locationuri=locationuri,
+                           location=location,
+                           date=date,
+                           source=source,
+                           sampletype=sampletype,
+                           institute=institute,
+                           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
diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css
index bc4f705..76a1755 100644
--- a/bh20simplewebuploader/static/main.css
+++ b/bh20simplewebuploader/static/main.css
@@ -506,3 +506,30 @@ div.status {
     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);
 }
+
+.flex-container {
+    display: flex;
+    flex-direction: row;
+    flex-wrap: wrap;
+    justify-content: space-evenly;
+}
+
+#twitter-feed {
+    background-color: #f5f8fa;
+    max-height: 440px;
+    max-width: 500px;
+    overflow-y: auto;
+    padding: 20px;
+    margin-left: auto;
+    margin-right: auto;
+}
+
+
+#twitter-feed ul {
+    list-style-type: none;
+}
+
+#twitter-feed ul li {
+    border-bottom: 2px solid white;
+    padding-bottom: 20px;
+}
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 89bc603..6cc0d9f 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -68,6 +68,12 @@ function fetchHTMLTable(apiEndPoint) {
             htmlString="<table>"
             for (var i=0; i<data.length;i++) {
                 let url = data[i]["key"];
+                continents = ["Q538", "Q48", "Q49", "Q18", "Q15", "Q27611" ];
+                node = url.split("/").pop();
+                console.log(continents.includes(node));
+                if (url.includes("wikidata") && !continents.includes(node)) {
+                    url = "http://covid19.genenetwork.org/location?label="+url ;
+                }
                 let label = data[i]["label"];
                 htmlString=htmlString+"<tr><td><a href=\""+url+"\">"+label+"</a></td><td>"+data[i]["count"]+"<td></tr>"
             }
diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html
index 88ce4c3..fa08f5b 100644
--- a/bh20simplewebuploader/templates/blog.html
+++ b/bh20simplewebuploader/templates/blog.html
@@ -9,12 +9,11 @@
     {{ embed|safe }}
     <hr>
 
-    <h1>Other blog entries</h1>
+    <h1>Other documents</h1>
 
     {% else %}
-    {% include 'blurb.html' %}
 
-    <h2>BLOG Entries:</h2>
+    <h2>Documents:</h2>
     {% endif %}
 
     <section class="blog-entries">
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
index 77d2fb6..be948f6 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -22,9 +22,27 @@
                     or <a href="/apidoc">REST API</a>. For more
                     information see the <a href="/about">FAQ!</a>.
                   </p>
-      <section id="map_view" class="map">
-        <div id="mapid"></div>
-      </section>
+
+                  <section class="flex-container">
+                      <div id="map_view" class="map">
+                          <div id="mapid"></div>
+                      </div>
+                      <div id="twitter-feed">
+                          <ul>
+                              {% for tweet in tweets|sort(reverse=true, attribute="timeposted")%}
+                              <li>
+                                  <p class="tweet">
+                                      {{ tweet.tweet|urlize(40, target="_blank") }} <br/>
+                                      by {{ tweet.author }}
+                                  </p>
+                                  <small class="timeposted">
+                                      {{ tweet.timeposted }}
+                                  </small>
+                              </li>
+                              {% endfor %}
+                          </ul>
+                      </div>
+                  </section>
 
                   <a href="https://projectredcap.org/"><img class="img-right" src="static/image/REDCap.png" /></a>
                   <p>
@@ -73,10 +91,11 @@
                     URI's</a>
                     for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a>
                     and machine readable metadata. For examples of
-                    use, see the <a href="/blog">BLOG</a>.
+                    use, see the <a href="/blog">docs</a>.
                   </p>
                 </div>
-        </section>
+              </section>
+
 
       {% include 'footer.html' %}
 
diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html
index 5d5fdc8..8e6ef52 100644
--- a/bh20simplewebuploader/templates/menu.html
+++ b/bh20simplewebuploader/templates/menu.html
@@ -6,7 +6,7 @@
     <a href="/status" class="{{ 'active' if menu=='STATUS' }}">STATUS</a>
     <a href="/demo" class="{{ 'active' if menu=='DEMO' }}">DEMO</a>
     <a href="/export" class="{{ 'active' if menu=='EXPORT' }}">EXPORT</a>
-    <a href="/blog" class="{{ 'active' if menu=='BLOG' }}">BLOG</a>
+    <a href="/blog" class="{{ 'active' if menu=='BLOG' }}">DOCS</a>
     <a href="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a>
     <a href="/contact" class="{{ 'active' if menu=='CONTACT' }}">CONTACT</a>
     <a href="javascript:void(0);" class="icon" onclick="myFunction()">
diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html
index fc52f13..4c50fb9 100644
--- a/bh20simplewebuploader/templates/resource.html
+++ b/bh20simplewebuploader/templates/resource.html
@@ -10,8 +10,8 @@
 	<p><a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-5ct8p1i1wrgyjvp#Data_collections">All sequences project</a></p>
 	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.fasta">All sequences (FASTA) relabled and deduplicated</a></p>
 	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p>
-	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p>
-	<p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p>
+	<!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p> -->
+	<!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p> -->
 	<!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.ttl.xz">All sequences in RDF using spodgi</a> - <a href="https://github.com/pangenome/spodgi">More about spodgi</a></p> -->