Wiring up export function

author: Pjotr Prins 2020-07-19 09:11:41 +0100
committer: Pjotr Prins 2020-07-19 09:11:41 +0100
commit: 7b2d388dbed11384c6a388a5437cca0b8f2914fd (patch)
tree: f2707c6811948b9c6adc63534ff456266508c109
parent: 0e4cb2c14b62ed4f39271c6006a99cea954fc688 (diff)
download: bh20-seq-resource-7b2d388dbed11384c6a388a5437cca0b8f2914fd.tar.gz
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bh20-seq-resource-7b2d388dbed11384c6a388a5437cca0b8f2914fd.zip
7 files changed, 141 insertions, 43 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 2c360e1..b88055f 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -630,6 +630,10 @@ def validated_page():
     validated_table(output, validated)
     return render_template('validated.html', table=Markup(output.getvalue()), menu='STATUS')
 
+@app.route('/export')
+def export_page():
+    return render_template('export.html',menu='EXPORT')
+
 @app.route('/demo')
 def demo_page():
     return render_template('demo.html',menu='DEMO',load_map=True)
@@ -685,6 +689,11 @@ def getCountDB():
     # print(result, file=sys.stderr)
     return jsonify({'sequences': int(result[0]["num"]["value"])})
 
+# Execute a 'global search'
+@app.route('/api/search', methods=['GET'])
+def search():
+    return jsonify(["TESTME"])
+
 @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 1633c25..dc0864b 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -21,8 +21,6 @@ function fetchAPI(apiEndPoint) {
         .then(data => {
             console.log(data);
         });
-    document.getElementById("map_view").classList.add("invisible");
-    document.getElementById("loader").classList.remove("invisible");
 }
 
 // Copy from function above but now output HTML table instead of plain json
@@ -51,7 +49,13 @@ function fetchHTMLTable(apiEndPoint) {
 }
 
 
-let search = () => {
+/* Fetch record info using a 'global search' */
+let searchGlobal = () => {
+    let m =  document.getElementById('search-input').value;
+    fetchAPI(scriptRoot + "/api/search?s=" + encodeURIComponent(m));
+}
+
+let searchSeq = () => {
   let m =  document.getElementById('search-input').value;
   fetchAPI(scriptRoot + "/api/getDetailsForSeq?seq=" + encodeURIComponent(m));
 }
diff --git a/bh20simplewebuploader/templates/export.html b/bh20simplewebuploader/templates/export.html
new file mode 100644
index 0000000..f105290
--- /dev/null
+++ b/bh20simplewebuploader/templates/export.html
@@ -0,0 +1,41 @@
+<!DOCTYPE html>
+<html>
+  {% include 'header.html' %}
+  <body>
+    {% include 'banner.html' %}
+    {% include 'menu.html' %}
+
+    <h1>Export Data</h1>
+    <section class="blog">
+
+    COVID-19 PubSeq allows for exporting forms and data for other
+    services.
+
+    <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:
+    </p>
+
+    <div class="search">
+      <input id="search-input" type="search" placeholder="e.g. MT246484" required>
+      <button class="button search-button" type="submit" onclick="searchGlobal()">
+        <span class="icon ion-search">
+          <span class="sr-only">Search</span>
+        </span>
+      </button>
+    </div>
+
+    </section>
+
+    {% include 'footer.html' %}
+
+    <script type="text/javascript">
+      let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
+    </script>
+  </body>
+
+</html>
diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html
index 0f6003f..d408171 100644
--- a/bh20simplewebuploader/templates/menu.html
+++ b/bh20simplewebuploader/templates/menu.html
@@ -5,6 +5,7 @@
     <a href="/upload" class="{{ 'active' if menu=='UPLOAD' }}">UPLOAD</a>
     <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="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a>
     <a href="javascript:void(0);" class="icon" onclick="myFunction()">
diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html
index 0e6136c..5fd86d1 100644
--- a/doc/blog/using-covid-19-pubseq-part1.html
+++ b/doc/blog/using-covid-19-pubseq-part1.html
@@ -3,7 +3,7 @@
 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
 <head>
-<!-- 2020-07-17 Fri 05:05 -->
+<!-- 2020-07-19 Sun 02:32 -->
 <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <title>COVID-19 PubSeq (part 1)</title>
@@ -248,20 +248,20 @@ for the JavaScript code in this tag.
 <h2>Table of Contents</h2>
 <div id="text-table-of-contents">
 <ul>
-<li><a href="#org0db5db0">1. What does this mean?</a></li>
-<li><a href="#orge5267fd">2. Fetch sequence data</a></li>
-<li><a href="#orgfbd3adc">3. Predicates</a></li>
-<li><a href="#org08e70e1">4. Fetch submitter info and other metadata</a></li>
-<li><a href="#org9194557">5. Fetch all sequences from Washington state</a></li>
-<li><a href="#org76317ad">6. Discussion</a></li>
-<li><a href="#orgeb871a1">7. Acknowledgements</a></li>
+<li><a href="#orgb852bf7">1. What does this mean?</a></li>
+<li><a href="#orge6db105">2. Fetch sequence data</a></li>
+<li><a href="#orgf3b8001">3. Predicates</a></li>
+<li><a href="#org11097b0">4. Fetch submitter info and other metadata</a></li>
+<li><a href="#org4f8467e">5. Fetch all sequences from Washington state</a></li>
+<li><a href="#orge9b18e2">6. Discussion</a></li>
+<li><a href="#orga0badf8">7. Acknowledgements</a></li>
 </ul>
 </div>
 </div>
 
 
-<div id="outline-container-org0db5db0" class="outline-2">
-<h2 id="org0db5db0"><span class="section-number-2">1</span> What does this mean?</h2>
+<div id="outline-container-orgb852bf7" class="outline-2">
+<h2 id="orgb852bf7"><span class="section-number-2">1</span> What does this mean?</h2>
 <div class="outline-text-2" id="text-1">
 <p>
 This means that when someone uploads a SARS-CoV-2 sequence using one
@@ -313,9 +313,8 @@ initiative!
 </div>
 </div>
 
-
-<div id="outline-container-orge5267fd" class="outline-2">
-<h2 id="orge5267fd"><span class="section-number-2">2</span> Fetch sequence data</h2>
+<div id="outline-container-orge6db105" class="outline-2">
+<h2 id="orge6db105"><span class="section-number-2">2</span> Fetch sequence data</h2>
 <div class="outline-text-2" id="text-2">
 <p>
 The latest run of the pipeline can be viewed <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">here</a>. Each of these
@@ -339,8 +338,8 @@ these identifiers throughout.
 </div>
 </div>
 
-<div id="outline-container-orgfbd3adc" class="outline-2">
-<h2 id="orgfbd3adc"><span class="section-number-2">3</span> Predicates</h2>
+<div id="outline-container-orgf3b8001" class="outline-2">
+<h2 id="orgf3b8001"><span class="section-number-2">3</span> Predicates</h2>
 <div class="outline-text-2" id="text-3">
 <p>
 To explore an RDF dataset, the first query we can do is open and gets
@@ -446,15 +445,18 @@ select (COUNT(distinct ?dataset) as ?num)
 }
 </pre>
 </div>
+
+<p>
+Run this <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;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&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">query</a>.
+</p>
 </div>
 </div>
 
-
-<div id="outline-container-org08e70e1" class="outline-2">
-<h2 id="org08e70e1"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2>
+<div id="outline-container-org11097b0" class="outline-2">
+<h2 id="org11097b0"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2>
 <div class="outline-text-2" id="text-4">
 <p>
-To get dataests with submitters we can do the above
+To get datasets with submitters we can do the above
 </p>
 
 <div class="org-src-container">
@@ -468,6 +470,10 @@ select distinct ?dataset ?p ?submitter
 </div>
 
 <p>
+Run this <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fdataset+%3Fp+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">query</a>.
+</p>
+
+<p>
 Tells you one submitter is "Roychoudhury,P.;Greninger,A.;Jerome,K."
 with a URL <a href="http://purl.obolibrary.org/obo/NCIT_C42781">predicate</a> (<a href="http://purl.obolibrary.org/obo/NCIT_C42781">http://purl.obolibrary.org/obo/NCIT_C42781</a>)
 explaining "The individual who is responsible for the content of a
@@ -526,6 +532,10 @@ select distinct ?sid ?sample ?p1 ?dataset ?submitter
 </div>
 
 <p>
+Run <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=%0D%0APREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fsid+%3Fsample+%3Fp1+%3Fdataset+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter+.%0D%0A+++FILTER%28CONTAINS%28%3Fsubmitter%2C%22Roychoudhury%22%29%29+.%0D%0A+++%3Fdataset+pubseq%3Asample+%3Fsid+.%0D%0A+++%3Fsid+%3Fp1+%3Fsample%0D%0A%7D%0D%0A&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">query</a>.
+</p>
+
+<p>
 which shows pretty much <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fsid+%3Fsample+%3Fp1+%3Fdataset+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter+.%0D%0A+++FILTER%28CONTAINS%28%3Fsubmitter%2C%22Roychoudhury%22%29%29+.%0D%0A+++%3Fdataset+pubseq%3Asample+%3Fsid+.%0D%0A+++%3Fsid+%3Fp1+%3Fsample%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">everything known</a> about their submissions in
 this database. Let's focus on one sample "MT326090.1" with predicate
 <a href="http://semanticscience.org/resource/SIO_000115">http://semanticscience.org/resource/SIO_000115</a>.
@@ -543,21 +553,26 @@ select distinct ?sample ?p ?o
 </div>
 
 <p>
-This <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT326090.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">query</a> tells us the sample was submitted "2020-03-21" and
+Run <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=%0D%0APREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT326090.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">query</a>.
+</p>
+
+<p>
+This query tells us the sample was submitted "2020-03-21" and
 originates from <a href="http://www.wikidata.org/entity/Q30">http://www.wikidata.org/entity/Q30</a>, i.e., the USA and
 is a biospecimen collected from the back of the throat by swabbing.
-We can track it back to the original GenBank <a href="http://identifiers.org/insdc/MT326090.1#sequence">submission</a>.
+We can track it back to the original GenBank <a href="http://identifiers.org/insdc/MT326090.1#sequence">submission</a> using the
+<a href="http://identifiers.org/insdc/MT326090.1">http://identifiers.org/insdc/MT326090.1</a> link.
 </p>
 
 <p>
 We have also added country and label data to make it a bit easier
-to view/query the database.
+to view/query the database and place the sequence on the <a href="http://covid19.genenetwork.org/">map</a>.
 </p>
 </div>
 </div>
 
-<div id="outline-container-org9194557" class="outline-2">
-<h2 id="org9194557"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2>
+<div id="outline-container-org4f8467e" class="outline-2">
+<h2 id="org4f8467e"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2>
 <div class="outline-text-2" id="text-5">
 <p>
 Now we know how to get at the origin we can do it the other way round
@@ -574,8 +589,8 @@ and fetch all sequences referring to Washington state
 </div>
 
 <p>
-which lists 300 sequences originating from Washington state! Which is almost
-half of the set coming out of GenBank.
+which lists 300 sequences originating from Washington state! Which in
+April was almost half of the set coming out of GenBank.
 </p>
 
 <p>
@@ -591,12 +606,15 @@ entity is <a href="https://www.wikidata.org/wiki/Q43">Q43</a>:
 }
 </pre>
 </div>
+
+<p>
+Run <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=%0D%0Aselect+%3Fseq+%3Fsample%0D%0A%7B%0D%0A++++%3Fseq+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2Fsample%3E+%3Fsample+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00000448%3E+%3Chttp%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ43%3E%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">query</a>.
+</p>
 </div>
 </div>
 
-
-<div id="outline-container-org76317ad" class="outline-2">
-<h2 id="org76317ad"><span class="section-number-2">6</span> Discussion</h2>
+<div id="outline-container-orge9b18e2" class="outline-2">
+<h2 id="orge9b18e2"><span class="section-number-2">6</span> Discussion</h2>
 <div class="outline-text-2" id="text-6">
 <p>
 The public sequence uploader collects sequences, raw data and
@@ -607,8 +625,8 @@ referenced in publications and origins are citeable.
 </div>
 </div>
 
-<div id="outline-container-orgeb871a1" class="outline-2">
-<h2 id="orgeb871a1"><span class="section-number-2">7</span> Acknowledgements</h2>
+<div id="outline-container-orga0badf8" class="outline-2">
+<h2 id="orga0badf8"><span class="section-number-2">7</span> Acknowledgements</h2>
 <div class="outline-text-2" id="text-7">
 <p>
 The overall effort was due to magnificent freely donated input by a
@@ -623,7 +641,7 @@ Garrison this initiative would not have existed!
 </div>
 </div>
 <div id="postamble" class="status">
-<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-17 Fri 05:02</small>.
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-19 Sun 02:32</small>.
 </div>
 </body>
 </html>
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org
index 0fd5589..9c8a1c0 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -60,7 +60,6 @@ graph in triples. Soon we will at multi sequence alignments (MSA) and
 more. Anyone can contribute data, tools and workflows to this
 initiative!
 
-
 * Fetch sequence data
 
 The latest run of the pipeline can be viewed [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][here]]. Each of these
@@ -162,10 +161,11 @@ select (COUNT(distinct ?dataset) as ?num)
 }
 #+end_src
 
+Run this [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&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+][query]].
 
 * Fetch submitter info and other metadata
 
-To get dataests with submitters we can do the above
+To get datasets with submitters we can do the above
 
 #+begin_src sql
 PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
@@ -176,6 +176,8 @@ select distinct ?dataset ?p ?submitter
 }
 #+end_src
 
+Run this [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fdataset+%3Fp+%3Fsubmitter%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+][query]].
+
 Tells you one submitter is "Roychoudhury,P.;Greninger,A.;Jerome,K."
 with a URL [[http://purl.obolibrary.org/obo/NCIT_C42781][predicate]] (http://purl.obolibrary.org/obo/NCIT_C42781)
 explaining "The individual who is responsible for the content of a
@@ -223,6 +225,8 @@ select distinct ?sid ?sample ?p1 ?dataset ?submitter
 }
 #+end_src
 
+Run [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fsid+%3Fsample+%3Fp1+%3Fdataset+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter+.%0D%0A+++FILTER%28CONTAINS%28%3Fsubmitter%2C%22Roychoudhury%22%29%29+.%0D%0A+++%3Fdataset+pubseq%3Asample+%3Fsid+.%0D%0A+++%3Fsid+%3Fp1+%3Fsample%0D%0A%7D%0D%0A&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]].
+
 which shows pretty much [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fsid+%3Fsample+%3Fp1+%3Fdataset+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter+.%0D%0A+++FILTER%28CONTAINS%28%3Fsubmitter%2C%22Roychoudhury%22%29%29+.%0D%0A+++%3Fdataset+pubseq%3Asample+%3Fsid+.%0D%0A+++%3Fsid+%3Fp1+%3Fsample%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][everything known]] about their submissions in
 this database. Let's focus on one sample "MT326090.1" with predicate
 http://semanticscience.org/resource/SIO_000115.
@@ -237,13 +241,16 @@ select distinct ?sample ?p ?o
 }
 #+end_src
 
-This [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT326090.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]] tells us the sample was submitted "2020-03-21" and
+Run [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT326090.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]].
+
+This query tells us the sample was submitted "2020-03-21" and
 originates from http://www.wikidata.org/entity/Q30, i.e., the USA and
 is a biospecimen collected from the back of the throat by swabbing.
-We can track it back to the original GenBank [[http://identifiers.org/insdc/MT326090.1#sequence][submission]].
+We can track it back to the original GenBank [[http://identifiers.org/insdc/MT326090.1#sequence][submission]] using the
+http://identifiers.org/insdc/MT326090.1 link.
 
 We have also added country and label data to make it a bit easier
-to view/query the database.
+to view/query the database and place the sequence on the [[http://covid19.genenetwork.org/][map]].
 
 * Fetch all sequences from Washington state
 
@@ -258,8 +265,8 @@ select ?seq ?sample
 }
 #+end_src
 
-which lists 300 sequences originating from Washington state! Which is almost
-half of the set coming out of GenBank.
+which lists 300 sequences originating from Washington state! Which in
+April was almost half of the set coming out of GenBank.
 
 Likewise to list all sequences from Turkey we can find the wikidata
 entity is [[https://www.wikidata.org/wiki/Q43][Q43]]:
@@ -272,6 +279,7 @@ select ?seq ?sample
 }
 #+end_src
 
+Run [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0Aselect+%3Fseq+%3Fsample%0D%0A%7B%0D%0A++++%3Fseq+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2Fsample%3E+%3Fsample+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00000448%3E+%3Chttp%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ43%3E%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]].
 
 * Discussion
 
diff --git a/doc/blog/using-covid-19-pubseq-part6.org b/doc/blog/using-covid-19-pubseq-part6.org
index 8964700..6ee68bb 100644
--- a/doc/blog/using-covid-19-pubseq-part6.org
+++ b/doc/blog/using-covid-19-pubseq-part6.org
@@ -9,11 +9,26 @@
 
 
 * Table of Contents                                                     :TOC:noexport:
+ - [[#short-version][Short version]]
  - [[#generating-output-for-ebi][Generating output for EBI]]
  - [[#defining-the-ebi-study][Defining the EBI study]]
  - [[#define-the-ebi-sample][Define the EBI sample]]
  - [[#define-the-ebi-sequence][Define the EBI sequence]]
 
+* Short version
+
+PubSeq can export files that can be uploaded to EBI/ENA. This saves
+you work. Steps are:
+
+1. Register and account for EBI/ENA as explained [[https://ena-docs.readthedocs.io/en/latest/submit/general-guide.html][here]].
+2. Register a study online or use XML files discussed below
+3. Export a sample XML and push to EBI/ENA
+4. Zip sequence data and push to EBI/ENA
+
+Because PubSeq's metadata for is richer than the metadata EBI/ENA asks
+for, it is easy to generate and export the forms using the [[http://covid19.genenetwork.org/export][EXPORT]]
+page.
+
 * Generating output for EBI
 
 Would it not be great an uploader to PubSeq also can export samples
@@ -81,6 +96,8 @@ also a submission 'command' is required looking like
 
 #+END_SRC
 
+Working XML examples we tested can be found [[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/submit_ebi/example][here]].
+
 The webin system accepts such sources using a command like
 
 : curl -u username:password -F "SUBMISSION=@submission.xml" \
@@ -88,7 +105,7 @@ The webin system accepts such sources using a command like
 
 as described [[https://ena-docs.readthedocs.io/en/latest/submit/study/programmatic.html#submit-the-xmls-using-curl][here]]. Note that this is the test server. For the final
 version use www.ebi.ac.uk instead of wwwdev.ebi.ac.uk.  You may also
-need the --insecure switch to circumvent certificate checking.
+need the =--insecure= switch to circumvent certificate checking.
 
 /work in progress (WIP)/
author	Pjotr Prins	2020-07-19 09:11:41 +0100
committer	Pjotr Prins	2020-07-19 09:11:41 +0100
commit	7b2d388dbed11384c6a388a5437cca0b8f2914fd (patch)
tree	f2707c6811948b9c6adc63534ff456266508c109
parent	0e4cb2c14b62ed4f39271c6006a99cea954fc688 (diff)
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