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

3 files changed, 12 insertions, 9 deletions

diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index bf95832..024a101 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -50,10 +50,6 @@ let fetchAllaccessions = () => {
  * may not expect.
  */
 
-let uploadForm = document.getElementById('metadata_upload_form')
-let uploadFormSpot = document.getElementById('metadata_upload_form_spot')
-let fillForm = document.getElementById('metadata_fill_form')
-let fillFormSpot = document.getElementById('metadata_fill_form_spot')
 
 function setUploadMode() {
   // Make the upload form the one in use.
@@ -87,7 +83,6 @@ function setMode() {
 // have set the radio button to whatever the state was on last page load,
 // instead of the default state, without raising an event, and we have to
 // handle that.
-setMode()
 
 /**
  * Add another form field to the group this button is part of.
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index 2cbaf62..1227ca2 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -114,7 +114,7 @@
                         {% for record in fields %}
 
                         {% if 'heading' in record %}
-                        {% if loop.index > 1 and 2 < 3  %}
+                        {% if loop.index > 1 and 2 < 3  %} <!-- for emacs matching elements -->
                     </div>
                     {% endif %}
                     <div class="record"> <!-- from block, e.g. host fields -->
@@ -211,6 +211,12 @@
 
 <script type="text/javascript">
   let scriptRoot = {{ request.script_root|tojson|safe }};
+  let uploadForm = document.getElementById('metadata_upload_form')
+  let uploadFormSpot = document.getElementById('metadata_upload_form_spot')
+  let fillForm = document.getElementById('metadata_fill_form')
+  let fillFormSpot = document.getElementById('metadata_fill_form_spot')
+
+  setMode()
 
   document.addEventListener("DOMContentLoaded", function(){
       var count = fetch("/api/getCount")
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org
index 4b7ddc6..bca885d 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -138,10 +138,12 @@ select distinct ?dataset ?submitter
 }
 #+end_src
 
-which reads a bit better. We can also see the datasets. One of them submitted
-by University of Washington is
-is http://arvados.org/keep:00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta
+which reads a bit better. We can also see the [[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+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter%0D%0A%7D%0D%0A&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][submitted sequences]]. One
+of them submitted by University of Washington is
+http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/sequence.fasta
 (note the ID may have changed so pick one with above query).
+To see the submitted metadata replace sequence.fasta with metadata.yaml
+http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/metadata.yaml
 
 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