From 60212ade3721cc9eebc976d65c973ab6b690bd3e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 19 Jul 2020 10:47:07 +0100
Subject: Search table

---
 bh20simplewebuploader/main.py               | 21 ++++++++++++-
 bh20simplewebuploader/static/main.js        | 49 ++++++++++++++++++++++++++---
 bh20simplewebuploader/templates/export.html | 22 ++++++++++---
 3 files changed, 81 insertions(+), 11 deletions(-)

(limited to 'bh20simplewebuploader')

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index b88055f..48520fe 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -692,7 +692,26 @@ def getCountDB():
 # Execute a 'global search'
 @app.route('/api/search', methods=['GET'])
 def search():
-    return jsonify(["TESTME"])
+    s = request.args.get('s')
+    query = """
+    PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+    PREFIX sio: <http://semanticscience.org/resource/>
+    select distinct ?id ?seq
+    {
+    ?sample sio:SIO_000115 "%s" .
+    ?sample sio:SIO_000115 ?id .
+    ?seq pubseq:sample ?sample .
+    ?sample ?p ?o .
+    }
+    """ % s
+    payload = {'query': query, 'format': 'json'}
+    r = requests.get(baseURL, params=payload)
+    result = r.json()['results']['bindings']
+    print(result,file=sys.stderr);
+    return jsonify([{
+        'id': x['id']['value'],
+        'seq': x['seq']['value'],
+    } for x in result])
 
 @app.route('/api/getAllaccessions', methods=['GET'])
 def getAllaccessions():
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index dc0864b..8271d2c 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -2,6 +2,24 @@
  * Menu and navigation
  */
 
+/* Convert a list of table items to an HTML DIV table */
+function toDIVTable(rows) {
+    if (rows.length == 0)
+        html = "no results";
+    else {
+        html = '<div class="rTable">';
+        rows.forEach(row => {
+            html += '<div class="rTableRow">';
+            html += '  <div class="rTableCell">';
+            html += row["id"];
+            html += '  </div>';
+            html += '</div>';
+        });
+        html += '</div>';
+    }
+    document.getElementById("table").innerHTML = html;
+}
+
 /* Toggle between adding and removing the "responsive" class to topnav
  * when the user clicks on the icon */
 function myFunction() {
@@ -13,13 +31,16 @@ function myFunction() {
     }
 }
 
-function fetchAPI(apiEndPoint) {
+function fetchAPI(apiEndPoint,injectHTML=NULL) {
     fetch(scriptRoot + apiEndPoint)
         .then(response => {
+            console.log("* response",response);
             return response.json();
         })
         .then(data => {
-            console.log(data);
+            console.log("* data",data);
+            if (injectHTML)
+                injectHTML(data);
         });
 }
 
@@ -48,11 +69,29 @@ function fetchHTMLTable(apiEndPoint) {
         });
 }
 
+/* Fetch record info using a 'global search'. Returns for example
+
+[
+  {
+    "id": "MT326090.1",
+    "seq": "http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126/sequence.fasta"
+  },
+  {
+    "id": "MT326090.1",
+    "seq": "http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126/sequence.fasta"
+  }
+]
+
 
-/* Fetch record info using a 'global search' */
-let searchGlobal = () => {
+ */
+let searchGlobal = (toHTML) => {
     let m =  document.getElementById('search-input').value;
-    fetchAPI(scriptRoot + "/api/search?s=" + encodeURIComponent(m));
+    fetchAPI(scriptRoot + "/api/search?s=" + encodeURIComponent(m), toHTML);
+}
+
+// Same as above, but generates div table
+let searchGlobaltoDIVTable = () => {
+    searchGlobal(toDIVTable);
 }
 
 let searchSeq = () => {
diff --git a/bh20simplewebuploader/templates/export.html b/bh20simplewebuploader/templates/export.html
index f105290..1f0d9b7 100644
--- a/bh20simplewebuploader/templates/export.html
+++ b/bh20simplewebuploader/templates/export.html
@@ -11,24 +11,36 @@
     COVID-19 PubSeq allows for exporting forms and data for other
     services.
 
+    <h2>SPARQL</h2>
+
+    <p>
+      First of all, PubSeq exports a SPARQL endpoint
+      <a href="http://sparql.genenetwork.org/sparql/">here</a> that allows
+      you do do any query on the data. See this
+      <a href="/blog?id=using-covid-19-pubseq-part1">document</a> for
+      examples.
+    </p>
+
     <h2>Export EBI/ENA Forms</h2>
 
     <p>
-    Uploading data to EBI/ENA with PubSeq is described
-    <a href="/blog?id=using-covid-19-pubseq-part6">here</a>.
-    To export, first search for an uploaded entry through its
-    identifier:
+      Uploading data to EBI/ENA with PubSeq is described
+      <a href="/blog?id=using-covid-19-pubseq-part6">here</a>. To
+      export, first search for an uploaded entry through its
+      identifier:
     </p>
 
     <div class="search">
       <input id="search-input" type="search" placeholder="e.g. MT246484" required>
-      <button class="button search-button" type="submit" onclick="searchGlobal()">
+      <button class="button search-button" type="submit" onclick="searchGlobaltoDIVTable()">
         <span class="icon ion-search">
           <span class="sr-only">Search</span>
         </span>
       </button>
     </div>
 
+    <section id="table" />
+
     </section>
 
     {% include 'footer.html' %}
-- 
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