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

author: Pjotr Prins 2020-05-16 10:18:50 -0500
committer: Pjotr Prins 2020-05-16 10:18:50 -0500
commit: 89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4 (patch)
tree: a2cb50022c93b5f508d47b6ece99a0063c92687e
parent: fe56e0ddd8bf91b7cfb4be7562e6aa1ee4c9a285 (diff)
parent: 2d201e156d530e5e912252c4300245da382b846e (diff)
download: bh20-seq-resource-89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4.tar.gz
bh20-seq-resource-89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4.tar.lz
bh20-seq-resource-89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4.zip
4 files changed, 65 insertions, 9 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 1dff207..0ba43fd 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -424,6 +424,23 @@ def receive_files():
 ## but most likley you don't want to touch the queries, Cheers.
 baseURL='http://sparql.genenetwork.org/sparql/'
 
+@app.route('/api/getCount', methods=['GET'])
+def getCount():
+    query="""
+PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+select (COUNT(distinct ?dataset) as ?num)
+{
+   ?dataset pubseq:submitter ?id .
+   ?id ?p ?submitter
+}
+"""
+    payload = {'query': query, 'format': 'json'}
+    r = requests.get(baseURL, params=payload)
+    result = r.json()['results']['bindings']
+    # [{'num': {'type': 'typed-literal', 'datatype': 'http://www.w3.org/2001/XMLSchema#integer', 'value': '1352'}}]
+    # print(result, file=sys.stderr)
+    return jsonify({'sequences': int(result[0]["num"]["value"])})
+
 @app.route('/api/getAllaccessions', methods=['GET'])
 def getAllaccessions():
     query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ <http://edamontology.org/data_2091> ?value ]}"""
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 7084e1f..bf95832 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -18,6 +18,10 @@ let search = () => {
   fetchAPI(scriptRoot + "/api/getDetailsForSeq?seq=" + encodeURIComponent(m));
 }
 
+let fetchCount = () => {
+  fetchAPI("/api/getCount");
+}
+
 let fetchSEQBySpecimen = () => {
   fetchAPI("/api/getSEQCountbySpecimenSource");
 }
@@ -160,7 +164,6 @@ for (let button of document.getElementsByClassName('remove-field')) {
 }
 
 // Change the submit button after hitting
-
 function on_submit_button() {
     var elem = document.getElementById("submit");
     elem.value = "Submitting...";
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index 7d7cef8..2cbaf62 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -6,13 +6,14 @@
         <link href="/static/main.css" rel="stylesheet" type="text/css">
         <meta name="viewport" content="width=device-width, initial-scale=1">
         <title>Web uploader for Public SARS-CoV-2 Sequence Resource</title>
+        <script type="text/javascript" src="/static/main.js"></script>
     </head>
     <body>
       <section class="header">
       <div class="logo"><a href="http://covid-19.genenetwork.org/"><img src="static/image/coronasmallcomp.gif" width="150" title="COVID-19 image by Tyler Morgan-Wall"></a></div>
       <h1>Web uploader for Public SARS-CoV-2 Sequence Resource</h1>
 
-<small>Disabled until we got everything wired up</small>
+      <p>Database contains <span id="Counter"></span> public sequences!</p>
 
       </section>
 
@@ -209,9 +210,21 @@
 </div>
 
 <script type="text/javascript">
-    let scriptRoot = {{ request.script_root|tojson|safe }};
+  let scriptRoot = {{ request.script_root|tojson|safe }};
+
+  document.addEventListener("DOMContentLoaded", function(){
+      var count = fetch("/api/getCount")
+          .then((resp) => resp.json())
+          .then(function (data) {
+              count = data["sequences"];
+              console.log(count);
+              span = document.getElementById("Counter");
+              txt = document.createTextNode(count);
+              span.appendChild(txt);
+      });
+});
+
 </script>
 
-<script type="text/javascript" src="/static/main.js"></script>
-    </body>
+   </body>
 </html>
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org
index 617a01d..4b7ddc6 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -75,8 +75,10 @@ these identifiers throughout.
 
 * Predicates
 
-Lets look at all the predicates in the dataset by pasting
-the following in a SPARQL end point http://sparql.genenetwork.org/sparql/
+To explore an RDF dataset, the first query we can do is open and gets
+us a list.  Lets look at all the predicates in the dataset by pasting
+the following in a SPARQL end point
+http://sparql.genenetwork.org/sparql/
 
 #+begin_src sql
 select distinct ?p
@@ -86,9 +88,19 @@ select distinct ?p
 #+end_src
 
 you can ignore the openlink and w3 ones. To reduce results to a named
-graph set the default graph to
+graph set the default graph.
+To get a [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=select+distinct+%3Fg%0D%0A%7B%0D%0A++++GRAPH+%3Fg+%7B%3Fs+%3Fp+%3Fo%7D%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][list of graphs]] in the dataset, first do
+
+#+begin_src sql
+select distinct ?g
+{
+    GRAPH ?g {?s ?p ?o}
+}
+#+end_src
+
+Limiting search to metadata add
 http://covid-19.genenetwork.org/graph/metadata.ttl in the top input
-box. There you can find a predicate for submitter that looks like
+box. Now you can find a [[http://sparql.genenetwork.org/sparql/?default-graph-uri=http%3A%2F%2Fcovid-19.genenetwork.org%2Fgraph%2Fmetadata.ttl&query=select+distinct+%3Fp%0D%0A%7B%0D%0A+++%3Fo+%3Fp+%3Fs%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][predicate]] for submitter that looks like
 http://biohackathon.org/bh20-seq-schema#MainSchema/submitter.
 
 To list all submitters, try
@@ -131,6 +143,17 @@ by University of Washington is
 is http://arvados.org/keep:00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta
 (note the ID may have changed so pick one with above query).
 
+Now we got this far, lets [[http://sparql.genenetwork.org/sparql/?default-graph-uri=http%3A%2F%2Fcovid-19.genenetwork.org%2Fgraph%2Fmetadata.ttl&query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+%28COUNT%28distinct+%3Fdataset%29+as+%3Fnum%29%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter%0D%0A%7D+&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][count the datasets]] submitted with
+
+#+begin_src sql
+PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+select (COUNT(distinct ?dataset) as ?num)
+{
+   ?dataset pubseq:submitter ?id .
+   ?id ?p ?submitter
+}
+#+end_src
+
 
 * Fetch submitter info and other metadata
author	Pjotr Prins	2020-05-16 10:18:50 -0500
committer	Pjotr Prins	2020-05-16 10:18:50 -0500
commit	89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4 (patch)
tree	a2cb50022c93b5f508d47b6ece99a0063c92687e
parent	fe56e0ddd8bf91b7cfb4be7562e6aa1ee4c9a285 (diff)
parent	2d201e156d530e5e912252c4300245da382b846e (diff)
download	bh20-seq-resource-89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4.tar.gz bh20-seq-resource-89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4.tar.lz bh20-seq-resource-89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4.zip