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authorPjotr Prins2020-08-26 11:14:44 +0100
committerPjotr Prins2020-08-26 11:15:06 +0100
commit2acf6a3c466dd296966e2c2c6a7e104e4a40bf31 (patch)
tree799f46453a6d6db4a53863499b11936ad04f2235 /doc
parent02d761902d49491f5b85c117dcb37db072be034d (diff)
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Docs
Diffstat (limited to 'doc')
-rw-r--r--doc/blog/using-covid-19-pubseq-part1.html137
-rw-r--r--doc/blog/using-covid-19-pubseq-part1.org2
-rw-r--r--doc/blog/using-covid-19-pubseq-part2.html70
-rw-r--r--doc/blog/using-covid-19-pubseq-part2.org27
4 files changed, 144 insertions, 92 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html
index 5fd86d1..deeb749 100644
--- a/doc/blog/using-covid-19-pubseq-part1.html
+++ b/doc/blog/using-covid-19-pubseq-part1.html
@@ -3,10 +3,10 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
-<!-- 2020-07-19 Sun 02:32 -->
+<!-- 2020-08-26 Wed 05:02 -->
<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>
+<title>COVID-19 PubSeq - query metadata (part 1)</title>
<meta name="generator" content="Org mode" />
<meta name="author" content="Pjotr Prins" />
<style type="text/css">
@@ -243,25 +243,25 @@ for the JavaScript code in this tag.
</head>
<body>
<div id="content">
-<h1 class="title">COVID-19 PubSeq (part 1)</h1>
+<h1 class="title">COVID-19 PubSeq - query metadata (part 1)</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<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>
+<li><a href="#orga5382ca">1. What does this mean?</a></li>
+<li><a href="#orgf6c7763">2. Fetch sequence data</a></li>
+<li><a href="#org228a8d5">3. Predicates</a></li>
+<li><a href="#orgfb34172">4. Fetch submitter info and other metadata</a></li>
+<li><a href="#org16f6b8d">5. Fetch all sequences from Washington state</a></li>
+<li><a href="#org2a85986">6. Discussion</a></li>
+<li><a href="#orgcf3645c">7. Acknowledgements</a></li>
</ul>
</div>
</div>
-<div id="outline-container-orgb852bf7" class="outline-2">
-<h2 id="orgb852bf7"><span class="section-number-2">1</span> What does this mean?</h2>
+<div id="outline-container-orga5382ca" class="outline-2">
+<h2 id="orga5382ca"><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
@@ -274,24 +274,24 @@ expressed in a <a href="https://github.com/arvados/bh20-seq-resource/blob/master
type: record
fields:
host_species:
- doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens
+ doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_<span style="color: #8bc34a;">9606</span> for Homo sapiens
type: string
jsonldPredicate:
- _id: http://www.ebi.ac.uk/efo/EFO_0000532
- _type: "@id"
- noLinkCheck: true
+ _id: http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0000532</span>
+ _type: <span style="color: #9ccc65;">"@id"</span>
+ noLinkCheck: <span style="color: #8bc34a;">true</span>
host_sex:
doc: Sex of the host as defined in PATO, expect male () or female ()
type: string?
jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/PATO_0000047
- _type: "@id"
- noLinkCheck: true
+ _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000047</span>
+ _type: <span style="color: #9ccc65;">"@id"</span>
+ noLinkCheck: <span style="color: #8bc34a;">true</span>
host_age:
- doc: Age of the host as number (e.g. 50)
+ doc: Age of the host as number (e.g. <span style="color: #8bc34a;">50</span>)
type: int?
jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/PATO_0000011
+ _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000011</span>
</pre>
</div>
@@ -313,8 +313,8 @@ initiative!
</div>
</div>
-<div id="outline-container-orge6db105" class="outline-2">
-<h2 id="orge6db105"><span class="section-number-2">2</span> Fetch sequence data</h2>
+<div id="outline-container-orgf6c7763" class="outline-2">
+<h2 id="orgf6c7763"><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
@@ -338,8 +338,8 @@ these identifiers throughout.
</div>
</div>
-<div id="outline-container-orgf3b8001" class="outline-2">
-<h2 id="orgf3b8001"><span class="section-number-2">3</span> Predicates</h2>
+<div id="outline-container-org228a8d5" class="outline-2">
+<h2 id="org228a8d5"><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
@@ -349,7 +349,7 @@ the following in a SPARQL end point
</p>
<div class="org-src-container">
-<pre class="src src-sql">select distinct ?p
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p
{
?o ?p ?s
}
@@ -363,7 +363,7 @@ To get a <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;q
</p>
<div class="org-src-container">
-<pre class="src src-sql">select distinct ?g
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?g
{
GRAPH ?g {?s ?p ?o}
}
@@ -382,9 +382,9 @@ To list all submitters, try
</p>
<div class="org-src-container">
-<pre class="src src-sql">select distinct ?s
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s
{
- ?o &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/submitter&gt; ?s
+ ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter&gt;</a> ?s
}
</pre>
</div>
@@ -396,9 +396,9 @@ and by
</p>
<div class="org-src-container">
-<pre class="src src-sql">select distinct ?s
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s
{
- ?o &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/submitter&gt; ?id .
+ ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter&gt;</a> ?id .
?id ?p ?s
}
</pre>
@@ -414,8 +414,8 @@ To lift the full URL out of the query you can use a header like
</p>
<div class="org-src-container">
-<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-select distinct ?dataset ?submitter
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter
{
?dataset pubseq:submitter ?id .
?id ?p ?submitter
@@ -437,8 +437,8 @@ Now we got this far, lets <a href="http://sparql.genenetwork.org/sparql/?default
</p>
<div class="org-src-container">
-<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-select (COUNT(distinct ?dataset) as ?num)
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> (<span style="color: #ff8A65;">COUNT</span>(<span style="color: #fff59d;">distinct</span> ?dataset) <span style="color: #fff59d;">as</span> ?num)
{
?dataset pubseq:submitter ?id .
?id ?p ?submitter
@@ -452,16 +452,16 @@ Run this <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;q
</div>
</div>
-<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 id="outline-container-orgfb34172" class="outline-2">
+<h2 id="orgfb34172"><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 datasets with submitters we can do the above
</p>
<div class="org-src-container">
-<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-select distinct ?dataset ?p ?submitter
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?p ?submitter
{
?dataset pubseq:submitter ?id .
?id ?p ?submitter
@@ -486,12 +486,12 @@ Let's focus on one sample with
</p>
<div class="org-src-container">
-<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-select distinct ?dataset ?submitter
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter
{
?dataset pubseq:submitter ?id .
?id ?p ?submitter .
- FILTER(CONTAINS(?submitter,"Roychoudhury")) .
+ FILTER(<span style="color: #fff59d;">CONTAINS</span>(?submitter,"Roychoudhury")) .
}
</pre>
</div>
@@ -502,8 +502,8 @@ see if we can get a sample ID by listing sample predicates
</p>
<div class="org-src-container">
-<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-select distinct ?p
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p
{
?dataset ?p ?o .
?dataset pubseq:submitter ?id .
@@ -519,12 +519,12 @@ Let's zoom in on those of Roychoudhury with
<div class="org-src-container">
-<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-select distinct ?sid ?sample ?p1 ?dataset ?submitter
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sid ?sample ?p1 ?dataset ?submitter
{
?dataset pubseq:submitter ?id .
?id ?p ?submitter .
- FILTER(CONTAINS(?submitter,"Roychoudhury")) .
+ FILTER(<span style="color: #fff59d;">CONTAINS</span>(?submitter,"Roychoudhury")) .
?dataset pubseq:sample ?sid .
?sid ?p1 ?sample
}
@@ -542,9 +542,14 @@ this database. Let's focus on one sample "MT326090.1" with predicate
</p>
<div class="org-src-container">
-<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-PREFIX sio: &lt;http://semanticscience.org/resource/&gt;
-select distinct ?sample ?p ?o
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">#MainSchema/&gt;
+</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">PREFIX</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/"> sio: &lt;http://semanticscience.org/resource/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sample ?p ?o
{
?sample sio:SIO_000115 "MT326090.1" .
?sample ?p ?o .
@@ -571,8 +576,8 @@ to view/query the database and place the sequence on the <a href="http://covid19
</div>
</div>
-<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 id="outline-container-org16f6b8d" class="outline-2">
+<h2 id="org16f6b8d"><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
@@ -580,10 +585,13 @@ and fetch all sequences referring to Washington state
</p>
<div class="org-src-container">
-<pre class="src src-sql">select ?seq ?sample
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> ?seq ?sample
{
- ?seq &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
- ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223&gt;
+ ?seq <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223&gt;</a>
}
</pre>
</div>
@@ -599,10 +607,13 @@ entity is <a href="https://www.wikidata.org/wiki/Q43">Q43</a>:
</p>
<div class="org-src-container">
-<pre class="src src-sql">select ?seq ?sample
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> ?seq ?sample
{
- ?seq &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
- ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q43&gt;
+ ?seq <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q43">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q43">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q43">#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q43&gt;</a>
}
</pre>
</div>
@@ -613,8 +624,8 @@ Run <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=
</div>
</div>
-<div id="outline-container-orge9b18e2" class="outline-2">
-<h2 id="orge9b18e2"><span class="section-number-2">6</span> Discussion</h2>
+<div id="outline-container-org2a85986" class="outline-2">
+<h2 id="org2a85986"><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
@@ -625,8 +636,8 @@ referenced in publications and origins are citeable.
</div>
</div>
-<div id="outline-container-orga0badf8" class="outline-2">
-<h2 id="orga0badf8"><span class="section-number-2">7</span> Acknowledgements</h2>
+<div id="outline-container-orgcf3645c" class="outline-2">
+<h2 id="orgcf3645c"><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
@@ -641,7 +652,7 @@ 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 2020-07-19 Sun 02:32</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 2020-08-26 Wed 05:02</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 9c8a1c0..e41952d 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -1,4 +1,4 @@
-#+TITLE: COVID-19 PubSeq (part 1)
+#+TITLE: COVID-19 PubSeq - query metadata (part 1)
#+AUTHOR: Pjotr Prins
# C-c C-e h h publish
# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time)
diff --git a/doc/blog/using-covid-19-pubseq-part2.html b/doc/blog/using-covid-19-pubseq-part2.html
index b124c89..567980d 100644
--- a/doc/blog/using-covid-19-pubseq-part2.html
+++ b/doc/blog/using-covid-19-pubseq-part2.html
@@ -3,10 +3,10 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
-<!-- 2020-08-25 Tue 05:55 -->
+<!-- 2020-08-26 Wed 05:01 -->
<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 2)</title>
+<title>COVID-19 PubSeq - Arvados</title>
<meta name="generator" content="Org mode" />
<meta name="author" content="Pjotr Prins" />
<style type="text/css">
@@ -247,35 +247,44 @@ for the JavaScript code in this tag.
|
<a accesskey="H" href="http://covid19.genenetwork.org"> HOME </a>
</div><div id="content">
-<h1 class="title">COVID-19 PubSeq (part 2)</h1>
+<h1 class="title">COVID-19 PubSeq - Arvados</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#orgd3ae0e5">1. Finding output of workflows</a></li>
-<li><a href="#orgce95d40">2. The Arvados file interface</a></li>
-<li><a href="#org95f2c67">3. The PubSeq Arvados shell</a></li>
-<li><a href="#orgfba95f0">4. Wiring up CWL</a></li>
-<li><a href="#orgdf910f1">5. Using the Arvados API</a></li>
+<li><a href="#org6501d83">1. The Arvados Web Server</a></li>
+<li><a href="#orgcb7854f">2. The Arvados file interface</a></li>
+<li><a href="#orgc8c3ccd">3. The PubSeq Arvados shell</a></li>
+<li><a href="#org028c1b4">4. Wiring up CWL</a></li>
+<li><a href="#org7cdc8cc">5. Using the Arvados API</a></li>
+<li><a href="#org5961211">6. Troubleshooting</a></li>
</ul>
</div>
</div>
-<div id="outline-container-orgd3ae0e5" class="outline-2">
-<h2 id="orgd3ae0e5"><span class="section-number-2">1</span> Finding output of workflows</h2>
+<div id="outline-container-org6501d83" class="outline-2">
+<h2 id="org6501d83"><span class="section-number-2">1</span> The Arvados Web Server</h2>
<div class="outline-text-2" id="text-1">
<p>
We are using Arvados to run common workflow language (CWL) pipelines.
The most recent output is on display on a <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">web page</a> (with time stamp)
-and a full list is generated <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>. It is nice to start up, but for
-most users we need a dedicated and themed results page. People don't
-want to wade through thousands of output files!
+and a full output list is generated <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>.
+</p>
+
+<p>
+Arvados has a web front which allows navigation through input and output data,
+workflows and the output of analysis pipelines (here CWL workflows).
+</p>
+
+<p>
+ <img src="static/image/arvados-workflow-output.png" />
</p>
</div>
</div>
-<div id="outline-container-orgce95d40" class="outline-2">
-<h2 id="orgce95d40"><span class="section-number-2">2</span> The Arvados file interface</h2>
+
+<div id="outline-container-orgcb7854f" class="outline-2">
+<h2 id="orgcb7854f"><span class="section-number-2">2</span> The Arvados file interface</h2>
<div class="outline-text-2" id="text-2">
<p>
Arvados has the web server, but it also has a REST API and associated
@@ -352,8 +361,8 @@ arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839d
</div>
</div>
-<div id="outline-container-org95f2c67" class="outline-2">
-<h2 id="org95f2c67"><span class="section-number-2">3</span> The PubSeq Arvados shell</h2>
+<div id="outline-container-orgc8c3ccd" class="outline-2">
+<h2 id="orgc8c3ccd"><span class="section-number-2">3</span> The PubSeq Arvados shell</h2>
<div class="outline-text-2" id="text-3">
<p>
When you login to Arvados (you can request permission from us) it is
@@ -408,8 +417,8 @@ essentially <a href="https://github.com/arvados/bh20-seq-resource/blob/2baa88b76
</div>
</div>
-<div id="outline-container-orgfba95f0" class="outline-2">
-<h2 id="orgfba95f0"><span class="section-number-2">4</span> Wiring up CWL</h2>
+<div id="outline-container-org028c1b4" class="outline-2">
+<h2 id="org028c1b4"><span class="section-number-2">4</span> Wiring up CWL</h2>
<div class="outline-text-2" id="text-4">
<p>
In above script <code>bh20-seq-analyzer</code> you can see that the <a href="https://www.commonwl.org/">Common
@@ -450,8 +459,8 @@ For more see <a href="https://hpc.guix.info/blog/2019/01/creating-a-reproducible
</div>
</div>
-<div id="outline-container-orgdf910f1" class="outline-2">
-<h2 id="orgdf910f1"><span class="section-number-2">5</span> Using the Arvados API</h2>
+<div id="outline-container-org7cdc8cc" class="outline-2">
+<h2 id="org7cdc8cc"><span class="section-number-2">5</span> Using the Arvados API</h2>
<div class="outline-text-2" id="text-5">
<p>
Arvados provides a rich API for accessing internals of the Cloud
@@ -466,9 +475,26 @@ get a list of <a href="https://github.com/arvados/bh20-seq-resource/blob/2baa88b
</p>
</div>
</div>
+
+<div id="outline-container-org5961211" class="outline-2">
+<h2 id="org5961211"><span class="section-number-2">6</span> Troubleshooting</h2>
+<div class="outline-text-2" id="text-6">
+<p>
+When workflows have errors we should check the logs in Arvados.
+</p>
+
+<p>
+Go to the <a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-825x3r5vcs41dus">project</a> page for 'COVID-19-BH20 Shared Project' -&gt; 'Public
+Sequence Resource'. Click on analysis runs
+<a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56">https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56</a>
+and 'Subprojects'. Click one of the runs and then on 'Processes' and you'll
+see what parts failed.
+</p>
+</div>
+</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 2020-08-25 Tue 04:32</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 2020-08-26 Wed 05:01</small>.
</div>
</body>
</html>
diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org
index c44b5c7..4b827f5 100644
--- a/doc/blog/using-covid-19-pubseq-part2.org
+++ b/doc/blog/using-covid-19-pubseq-part2.org
@@ -1,4 +1,4 @@
-#+TITLE: COVID-19 PubSeq (part 2)
+#+TITLE: COVID-19 PubSeq - Arvados
#+AUTHOR: Pjotr Prins
# C-c C-e h h publish
# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time)
@@ -9,19 +9,24 @@
#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
* Table of Contents :TOC:noexport:
- - [[#finding-output-of-workflows][Finding output of workflows]]
+ - [[#the-arvados-web-server][The Arvados Web Server]]
- [[#the-arvados-file-interface][The Arvados file interface]]
- [[#the-pubseq-arvados-shell][The PubSeq Arvados shell]]
- [[#wiring-up-cwl][Wiring up CWL]]
- [[#using-the-arvados-api][Using the Arvados API]]
+ - [[#troubleshooting][Troubleshooting]]
-* Finding output of workflows
+* The Arvados Web Server
We are using Arvados to run common workflow language (CWL) pipelines.
The most recent output is on display on a [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][web page]] (with time stamp)
-and a full list is generated [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. It is nice to start up, but for
-most users we need a dedicated and themed results page. People don't
-want to wade through thousands of output files!
+and a full output list is generated [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]].
+
+Arvados has a web front which allows navigation through input and output data,
+workflows and the output of analysis pipelines (here CWL workflows).
+
+@@html: <img src="static/image/arvados-workflow-output.png" />@@
+
* The Arvados file interface
@@ -127,3 +132,13 @@ In above script ~bh20-seq-analyzer~ there are examples of querying the
[[https://doc.arvados.org/api/index.html][Arvados API]] using the [[https://pypi.org/project/arvados-python-client/][Python Arvados client and libraries]]. For example
get a list of [[https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L228][projects]] in Arvados. Main thing is to get the
~ARVADOS-API-HOST~ and ~ARVADOS-API-TOKEN~ right as is shown above.
+
+* Troubleshooting
+
+When workflows have errors we should check the logs in Arvados.
+
+Go to the [[https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-825x3r5vcs41dus][project]] page for 'COVID-19-BH20 Shared Project' -> 'Public
+Sequence Resource'. Click on analysis runs
+https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56
+and 'Subprojects'. Click one of the runs and then on 'Processes' and you'll
+see what parts failed.
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-21 18:02:37 +0000