alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2025-01-27 05:49:12 +01:00
Code Issues Projects Releases Wiki Activity

Add notes for 2021-11-08

Browse Source
This commit is contained in:
Alan Orth
2021-11-09 06:29:52 +02:00
parent b3df4ff58f
commit 9afe5c13f9
110 changed files with 1827 additions and 1737 deletions
Download Patch File Download Diff File Expand all files Collapse all files

310
docs/2021-03/index.html
View File

@ -34,7 +34,7 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst
"/>
<meta name="generator" content="Hugo 0.88.1" />
<meta name="generator" content="Hugo 0.89.2" />
@ -163,19 +163,19 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst
<ul>
<li>I looked at the number of connections in PostgreSQL and it&rsquo;s definitely high again:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ psql -c <span style="color:#e6db74">&#39;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;&#39;</span> | wc -l
1020
</code></pre><ul>
</code></pre></div><ul>
<li>I reported it to Atmire to take a look, on the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=851">same issue</a> we had been tracking this before</li>
<li>Abenet asked me to add a new ORCID for ILRI staff member Zoe Campbell</li>
<li>I added it to the controlled vocabulary and then tagged her existing items on CGSpace using my <code>add-orcid-identifier.py</code> script:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ cat 2021-03-04-add-zoe-campbell-orcid.csv
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ cat 2021-03-04-add-zoe-campbell-orcid.csv
dc.contributor.author,cg.creator.identifier
&quot;Campbell, Zoë&quot;,&quot;Zoe Campbell: 0000-0002-4759-9976&quot;
&quot;Campbell, Zoe A.&quot;,&quot;Zoe Campbell: 0000-0002-4759-9976&quot;
$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p 'fuuu'
</code></pre><ul>
&#34;Campbell, Zoë&#34;,&#34;Zoe Campbell: 0000-0002-4759-9976&#34;
&#34;Campbell, Zoe A.&#34;,&#34;Zoe Campbell: 0000-0002-4759-9976&#34;
$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p <span style="color:#e6db74">&#39;fuuu&#39;</span>
</code></pre></div><ul>
<li>I still need to do cleanup on the journal articles metadata
<ul>
<li>Peter sent me some cleanups but I can&rsquo;t use them in the search/replace format he gave</li>
@ -183,9 +183,9 @@ $ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT dspace_object_id AS id, text_value as &quot;cg.journal&quot; FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT dspace_object_id AS id, text_value as &#34;cg.journal&#34; FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
COPY 32087
</code></pre><ul>
</code></pre></div><ul>
<li>I used OpenRefine to remove all journal values that didn&rsquo;t have one of these values: ; ( )
<ul>
<li>Then I cloned the <code>cg.journal</code> field to <code>cg.volume</code> and <code>cg.issue</code></li>
@ -193,10 +193,10 @@ COPY 32087
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">value.partition(';')[0].trim() # to get journal names
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,&quot;$1&quot;) # to get journal volumes
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,&quot;$1&quot;) # to get journal issues
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">value.partition(&#39;;&#39;)[0].trim() # to get journal names
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,&#34;$1&#34;) # to get journal volumes
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,&#34;$1&#34;) # to get journal issues
</code></pre></div><ul>
<li>Then I uploaded the changes to CGSpace using <code>dspace metadata-import</code></li>
<li>Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
<ul>
@ -233,14 +233,14 @@ value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,&quot;$1&quot;) #
<ul>
<li>I migrated the Docker bind mount for the AReS Elasticsearch container to a Docker volume:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ docker-compose -f docker/docker-compose.yml down
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ docker-compose -f docker/docker-compose.yml down
$ docker volume create docker_esData_7
$ docker container create --name es_dummy -v docker_esData_7:/usr/share/elasticsearch/data:rw elasticsearch:7.6.2
$ docker cp docker/esData_7/nodes es_dummy:/usr/share/elasticsearch/data
$ docker rm es_dummy
# edit docker/docker-compose.yml to switch from bind mount to volume
$ docker-compose -f docker/docker-compose.yml up -d
</code></pre><ul>
</code></pre></div><ul>
<li>The trick is that when you create a volume like &ldquo;myvolume&rdquo; from a <code>docker-compose.yml</code> file, Docker will create it with the name &ldquo;docker_myvolume&rdquo;
<ul>
<li>If you create it manually on the command line with <code>docker volume create myvolume</code> then the name is literally &ldquo;myvolume&rdquo;</li>
@ -249,39 +249,39 @@ $ docker-compose -f docker/docker-compose.yml up -d
<li>I still need to make the changes to git master and add these notes to the pull request so Moayad and others can benefit</li>
<li>Delete the <code>openrxv-items-temp</code> index to test a fresh harvesting:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
</code></pre><h2 id="2021-03-05-1">2021-03-05</h2>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-temp&#39;</span>
</code></pre></div><h2 id="2021-03-05-1">2021-03-05</h2>
<ul>
<li>Check the results of the AReS harvesting from last night:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#39;</span>
{
&quot;count&quot; : 101761,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
&#34;count&#34; : 101761,
&#34;_shards&#34; : {
&#34;total&#34; : 1,
&#34;successful&#34; : 1,
&#34;skipped&#34; : 0,
&#34;failed&#34; : 0
}
}
</code></pre><ul>
</code></pre></div><ul>
<li>Set the current items index to read only and make a backup:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Type: application/json' -d' {&quot;settings&quot;: {&quot;index.blocks.write&quot;:true}}'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39; {&#34;settings&#34;: {&#34;index.blocks.write&#34;:true}}&#39;</span>
$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-03-05
</code></pre><ul>
</code></pre></div><ul>
<li>Delete the current items index and clone the temp one to it:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items'
$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items&#39;</span>
$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items-temp/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: true}}&#39;</span>
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items
</code></pre><ul>
</code></pre></div><ul>
<li>Then delete the temp and backup:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
{&quot;acknowledged&quot;:true}%
$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-03-05'
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-temp&#39;</span>
{&#34;acknowledged&#34;:true}%
$ curl -XDELETE <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-2021-03-05&#39;</span>
</code></pre></div><ul>
<li>I made some pull requests to OpenRXV:
<ul>
<li><a href="https://github.com/ilri/OpenRXV/pull/86">docker/docker-compose.yml: Use docker volumes</a></li>
@ -298,57 +298,57 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-03-05'
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/_alias/&#39;</span> | python -m json.tool | less
...
&quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {
&quot;openrxv-items&quot;: {}
&#34;openrxv-items-final&#34;: {
&#34;aliases&#34;: {
&#34;openrxv-items&#34;: {}
}
},
</code></pre><ul>
</code></pre></div><ul>
<li>But on AReS production <code>openrxv-items</code> has somehow become a concrete index:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/_alias/&#39;</span> | python -m json.tool | less
...
&quot;openrxv-items&quot;: {
&quot;aliases&quot;: {}
&#34;openrxv-items&#34;: {
&#34;aliases&#34;: {}
},
&quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {}
&#34;openrxv-items-final&#34;: {
&#34;aliases&#34;: {}
},
&quot;openrxv-items-temp&quot;: {
&quot;aliases&quot;: {}
&#34;openrxv-items-temp&#34;: {
&#34;aliases&#34;: {}
},
</code></pre><ul>
</code></pre></div><ul>
<li>I fixed the issue on production by cloning the <code>openrxv-items</code> index to <code>openrxv-items-final</code>, deleting <code>openrxv-items</code>, and then re-creating it as an alias:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: true}}&#39;</span>
$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-03-07
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ curl -XDELETE <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-final&#39;</span>
$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-final
$ curl -XDELETE 'http://localhost:9200/openrxv-items'
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{&quot;actions&quot; : [{&quot;add&quot; : { &quot;index&quot; : &quot;openrxv-items-final&quot;, &quot;alias&quot; : &quot;openrxv-items&quot;}}]}'
</code></pre><ul>
$ curl -XDELETE <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items&#39;</span>
$ curl -s -X POST <span style="color:#e6db74">&#39;http://localhost:9200/_aliases&#39;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;actions&#34; : [{&#34;add&#34; : { &#34;index&#34; : &#34;openrxv-items-final&#34;, &#34;alias&#34; : &#34;openrxv-items&#34;}}]}&#39;</span>
</code></pre></div><ul>
<li>Delete backups and remove read-only mode on <code>openrxv-items</code>:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-03-07'
$ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XDELETE <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-2021-03-07&#39;</span>
$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: false}}&#39;</span>
</code></pre></div><ul>
<li>Linode sent alerts about the CPU usage on CGSpace yesterday and the day before
<ul>
<li>Looking in the logs I see a few IPs making heavy usage on the REST API and XMLUI:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console"># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz /var/log/nginx/access.log.3.gz | grep -E '0[56]/Mar/2021' | goaccess --log-format=COMBINED -
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console"># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz /var/log/nginx/access.log.3.gz | grep -E <span style="color:#e6db74">&#39;0[56]/Mar/2021&#39;</span> | goaccess --log-format<span style="color:#f92672">=</span>COMBINED -
</code></pre></div><ul>
<li>I see the usual IPs for CCAFS and ILRI importer bots, but also <code>143.233.242.132</code> which appears to be for GARDIAN:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console"># zgrep '143.233.242.132' /var/log/nginx/access.log.1 | grep -c Delphi
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console"># zgrep <span style="color:#e6db74">&#39;143.233.242.132&#39;</span> /var/log/nginx/access.log.1 | grep -c Delphi
6237
# zgrep '143.233.242.132' /var/log/nginx/access.log.1 | grep -c -v Delphi
# zgrep <span style="color:#e6db74">&#39;143.233.242.132&#39;</span> /var/log/nginx/access.log.1 | grep -c -v Delphi
6418
</code></pre><ul>
</code></pre></div><ul>
<li>They seem to make requests twice, once with the Delphi user agent that we know and already mark as a bot, and once with a &ldquo;normal&rdquo; user agent
<ul>
<li>Looking in Solr I see they have been using this IP for awhile, as they have 100,000 hits going back into 2020</li>
@ -375,9 +375,9 @@ $ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Typ
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ psql -c <span style="color:#e6db74">&#39;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;&#39;</span> | wc -l
13
</code></pre><ul>
</code></pre></div><ul>
<li>On 2021-03-03 the PostgreSQL transactions started rising:</li>
</ul>
<p><img src="/cgspace-notes/2021/03/postgres_querylength_ALL-week.png" alt="PostgreSQL query length week"></p>
@ -409,10 +409,10 @@ $ curl -X PUT &quot;localhost:9200/openrxv-items/_settings&quot; -H 'Content-Typ
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items-final/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: true}}&#39;</span>
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-2021-03-08
# start harvesting on AReS
</code></pre><ul>
</code></pre></div><ul>
<li>As I saw on my local test instance, even when you cancel a harvesting, it replaces the <code>openrxv-items-final</code> index with whatever is in <code>openrxv-items-temp</code> automatically, so I assume it will do the same now</li>
</ul>
<h2 id="2021-03-09">2021-03-09</h2>
@ -434,8 +434,8 @@ $ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ ./ilri/doi-to-handle.py -i /tmp/dois.txt -o /tmp/handles.txt -db dspace -u dspace -p 'fuuu'
</code></pre><h2 id="2021-03-10">2021-03-10</h2>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ ./ilri/doi-to-handle.py -i /tmp/dois.txt -o /tmp/handles.txt -db dspace -u dspace -p <span style="color:#e6db74">&#39;fuuu&#39;</span>
</code></pre></div><h2 id="2021-03-10">2021-03-10</h2>
<ul>
<li>Colleagues from ICARDA asked about how we should handle ISI journals in CG Core, as CGSpace uses <code>cg.isijournal</code> and MELSpace uses <code>mel.impact-factor</code>
<ul>
@ -444,12 +444,12 @@ $ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items
</li>
<li>Peter said he doesn&rsquo;t see &ldquo;Source Code&rdquo; or &ldquo;Software&rdquo; in the <a href="https://cgspace.cgiar.org/handle/10568/1/search-filter?field=type">output type facet on the ILRI community</a>, but I see it on the home page, so I will try to do a full Discovery re-index:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
real 318m20.485s
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ time chrt -b <span style="color:#ae81ff">0</span> ionice -c2 -n7 nice -n19 dspace index-discovery -b
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>real 318m20.485s
user 215m15.196s
sys 2m51.529s
</code></pre><ul>
</code></pre></div><ul>
<li>Now I see ten items for &ldquo;Source Code&rdquo; in the facets&hellip;</li>
<li>Add GPL and MIT licenses to the list of licenses on CGSpace input form since we will start capturing more software and source code</li>
<li>Added the ability to check <code>dcterms.license</code> values against the SPDX licenses in the csv-metadata-quality tool
@ -467,34 +467,34 @@ sys 2m51.529s
<ul>
<li>Switch to linux-kvm kernel on linode20 and linode18:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console"># apt update &amp;&amp; apt full-upgrade
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console"># apt update <span style="color:#f92672">&amp;&amp;</span> apt full-upgrade
# apt install linux-kvm
# apt remove linux-generic linux-image-generic linux-headers-generic linux-firmware
# apt autoremove &amp;&amp; apt autoclean
# apt autoremove <span style="color:#f92672">&amp;&amp;</span> apt autoclean
# reboot
</code></pre><ul>
</code></pre></div><ul>
<li>Deploy latest changes from <code>6_x-prod</code> branch on CGSpace</li>
<li>Deploy latest changes from OpenRXV <code>master</code> branch on AReS</li>
<li>Last week Peter added OpenRXV to CGSpace: <a href="https://hdl.handle.net/10568/112982">https://hdl.handle.net/10568/112982</a></li>
<li>Back up the current <code>openrxv-items-final</code> index on AReS to start a new harvest:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items-final/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: true}}&#39;</span>
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-2021-03-14
$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
</code></pre><ul>
$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items-final/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: false}}&#39;</span>
</code></pre></div><ul>
<li>After the harvesting finished it seems the indexes got messed up again, as <code>openrxv-items</code> is an alias of <code>openrxv-items-temp</code> instead of <code>openrxv-items-final</code>:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/_alias/&#39;</span> | python -m json.tool | less
...
&quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {}
&#34;openrxv-items-final&#34;: {
&#34;aliases&#34;: {}
},
&quot;openrxv-items-temp&quot;: {
&quot;aliases&quot;: {
&quot;openrxv-items&quot;: {}
&#34;openrxv-items-temp&#34;: {
&#34;aliases&#34;: {
&#34;openrxv-items&#34;: {}
}
},
</code></pre><ul>
</code></pre></div><ul>
<li>Anyways, the number of items in <code>openrxv-items</code> seems OK and the AReS Explorer UI is working fine
<ul>
<li>I will have to manually fix the indexes before the next harvesting</li>
@ -535,54 +535,54 @@ $ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Conte
</li>
<li>Back up the current <code>openrxv-items-final</code> index to start a fresh AReS Harvest:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items-final/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: true}}&#39;</span>
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-2021-03-21
$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
</code></pre><ul>
$ curl -X PUT <span style="color:#e6db74">&#34;localhost:9200/openrxv-items-final/_settings&#34;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;settings&#34;: {&#34;index.blocks.write&#34;: false}}&#39;</span>
</code></pre></div><ul>
<li>Then start harvesting in the AReS Explorer admin UI</li>
</ul>
<h2 id="2021-03-22">2021-03-22</h2>
<ul>
<li>The harvesting on AReS yesterday completed, but somehow I have twice the number of items:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&amp;pretty'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-final/_count?q=*&amp;pretty&#39;</span>
{
&quot;count&quot; : 206204,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
&#34;count&#34; : 206204,
&#34;_shards&#34; : {
&#34;total&#34; : 1,
&#34;successful&#34; : 1,
&#34;skipped&#34; : 0,
&#34;failed&#34; : 0
}
}
</code></pre><ul>
</code></pre></div><ul>
<li>Hmmm and even my backup index has a strange number of items:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final-2021-03-21/_count?q=*&amp;pretty'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-final-2021-03-21/_count?q=*&amp;pretty&#39;</span>
{
&quot;count&quot; : 844,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
&#34;count&#34; : 844,
&#34;_shards&#34; : {
&#34;total&#34; : 1,
&#34;successful&#34; : 1,
&#34;skipped&#34; : 0,
&#34;failed&#34; : 0
}
}
</code></pre><ul>
</code></pre></div><ul>
<li>I deleted all indexes and re-created the openrxv-items alias:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{&quot;actions&quot; : [{&quot;add&quot; : { &quot;index&quot; : &quot;openrxv-items-final&quot;, &quot;alias&quot; : &quot;openrxv-items&quot;}}]}'
$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s -X POST <span style="color:#e6db74">&#39;http://localhost:9200/_aliases&#39;</span> -H <span style="color:#e6db74">&#39;Content-Type: application/json&#39;</span> -d<span style="color:#e6db74">&#39;{&#34;actions&#34; : [{&#34;add&#34; : { &#34;index&#34; : &#34;openrxv-items-final&#34;, &#34;alias&#34; : &#34;openrxv-items&#34;}}]}&#39;</span>
$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/_alias/&#39;</span> | python -m json.tool | less
...
&quot;openrxv-items-temp&quot;: {
&quot;aliases&quot;: {}
&#34;openrxv-items-temp&#34;: {
&#34;aliases&#34;: {}
},
&quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {
&quot;openrxv-items&quot;: {}
&#34;openrxv-items-final&#34;: {
&#34;aliases&#34;: {
&#34;openrxv-items&#34;: {}
}
}
</code></pre><ul>
</code></pre></div><ul>
<li>Then I started a new harvesting</li>
<li>I switched the Node.js in the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to v12 since v10 will cease to be supported soon
<ul>
@ -591,26 +591,26 @@ $ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
</li>
<li>The AReS harvest finally finished, with 1047 pages of items, but the <code>openrxv-items-final</code> index is empty and the <code>openrxv-items-temp</code> index has a 103,000 items:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty'
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#39;</span>
{
&quot;count&quot; : 103162,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
&#34;count&#34; : 103162,
&#34;_shards&#34; : {
&#34;total&#34; : 1,
&#34;successful&#34; : 1,
&#34;skipped&#34; : 0,
&#34;failed&#34; : 0
}
}
</code></pre><ul>
</code></pre></div><ul>
<li>I tried to clone the temp index to the final, but got an error:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
{&quot;error&quot;:{&quot;root_cause&quot;:[{&quot;type&quot;:&quot;resource_already_exists_exception&quot;,&quot;reason&quot;:&quot;index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists&quot;,&quot;index_uuid&quot;:&quot;LmxH-rQsTRmTyWex2d8jxw&quot;,&quot;index&quot;:&quot;openrxv-items-final&quot;}],&quot;type&quot;:&quot;resource_already_exists_exception&quot;,&quot;reason&quot;:&quot;index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists&quot;,&quot;index_uuid&quot;:&quot;LmxH-rQsTRmTyWex2d8jxw&quot;,&quot;index&quot;:&quot;openrxv-items-final&quot;},&quot;status&quot;:400}%
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
{&#34;error&#34;:{&#34;root_cause&#34;:[{&#34;type&#34;:&#34;resource_already_exists_exception&#34;,&#34;reason&#34;:&#34;index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists&#34;,&#34;index_uuid&#34;:&#34;LmxH-rQsTRmTyWex2d8jxw&#34;,&#34;index&#34;:&#34;openrxv-items-final&#34;}],&#34;type&#34;:&#34;resource_already_exists_exception&#34;,&#34;reason&#34;:&#34;index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists&#34;,&#34;index_uuid&#34;:&#34;LmxH-rQsTRmTyWex2d8jxw&#34;,&#34;index&#34;:&#34;openrxv-items-final&#34;},&#34;status&#34;:400}%
</code></pre></div><ul>
<li>I looked in the Docker logs for Elasticsearch and saw a few memory errors:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">java.lang.OutOfMemoryError: Java heap space
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">java.lang.OutOfMemoryError: Java heap space
</code></pre></div><ul>
<li>According to <code>/usr/share/elasticsearch/config/jvm.options</code> in the Elasticsearch container the default JVM heap is 1g
<ul>
<li>I see the running Java process has <code>-Xms 1g -Xmx 1g</code> in its process invocation so I guess that it must be indeed using 1g</li>
@ -622,20 +622,20 @@ $ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console"> &quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {}
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console"> &#34;openrxv-items-final&#34;: {
&#34;aliases&#34;: {}
},
&quot;openrxv-items-temp&quot;: {
&quot;aliases&quot;: {
&quot;openrxv-items&quot;: {}
&#34;openrxv-items-temp&#34;: {
&#34;aliases&#34;: {
&#34;openrxv-items&#34;: {}
}
},
</code></pre><h2 id="2021-03-23">2021-03-23</h2>
</code></pre></div><h2 id="2021-03-23">2021-03-23</h2>
<ul>
<li>For reference you can also get the Elasticsearch JVM stats from the API:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_nodes/jvm?human' | python -m json.tool
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/_nodes/jvm?human&#39;</span> | python -m json.tool
</code></pre></div><ul>
<li>I re-deployed AReS with 1.5GB of heap using the <code>ES_JAVA_OPTS</code> environment variable
<ul>
<li>It turns out that this <em>is</em> the recommended way to set the heap: <a href="https://www.elastic.co/guide/en/elasticsearch/reference/7.6/jvm-options.html">https://www.elastic.co/guide/en/elasticsearch/reference/7.6/jvm-options.html</a></li>
@ -644,8 +644,8 @@ $ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
<li>Then I fixed the aliases to make sure <code>openrxv-items</code> was an alias of <code>openrxv-items-final</code>, similar to how I did a few weeks ago</li>
<li>I re-created the temp index:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -XPUT 'http://localhost:9200/openrxv-items-temp'
</code></pre><h2 id="2021-03-24">2021-03-24</h2>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ curl -XPUT <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-temp&#39;</span>
</code></pre></div><h2 id="2021-03-24">2021-03-24</h2>
<ul>
<li>Atmire responded to the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=934">ticket about the Duplicate Checker</a>
<ul>
@ -659,35 +659,35 @@ $ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console"># du -s /home/dspacetest.cgiar.org/solr/statistics
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console"># du -s /home/dspacetest.cgiar.org/solr/statistics
57861236 /home/dspacetest.cgiar.org/solr/statistics
</code></pre><ul>
</code></pre></div><ul>
<li>I applied their changes to <code>config/spring/api/atmire-cua-update.xml</code> and started the duplicate processor:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx4096m'
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -r 1000 -c statistics -t 12
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ export JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#39;-Dfile.encoding=UTF-8 -Xmx4096m&#39;</span>
$ chrt -b <span style="color:#ae81ff">0</span> dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -r <span style="color:#ae81ff">1000</span> -c statistics -t <span style="color:#ae81ff">12</span>
</code></pre></div><ul>
<li>The default number of records per query is 10,000, which caused memory issues, so I will try with 1000 (Atmire used 100, but that seems too low!)</li>
<li>Hah, I still got a memory error after only a few minutes:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">...
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">...
Run 1 —  80% — 5,000/6,263 docs — 25s — 6m 31s
Exception: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
</code></pre><ul>
</code></pre></div><ul>
<li>I guess we really do have to use <code>-r 100</code></li>
<li>Now the thing runs for a few minutes and &ldquo;finishes&rdquo;:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -r 100 -c statistics -t 12
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ chrt -b <span style="color:#ae81ff">0</span> dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -r <span style="color:#ae81ff">100</span> -c statistics -t <span style="color:#ae81ff">12</span>
Loading @mire database changes for module MQM
Changes have been processed
*************************
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>*************************
* Update Script Started *
*************************
Run 1
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>Run 1
Start updating Solr Storage Reports | Wed Mar 24 14:42:17 CET 2021
Deleting old storage docs from Solr... | Wed Mar 24 14:42:17 CET 2021
Done. | Wed Mar 24 14:42:17 CET 2021
@ -752,12 +752,12 @@ Run 1 —  97% — 4,700/4,824 docs — 2s — 5m 49s
Run 1 — 100% — 4,800/4,824 docs — 2s — 5m 51s
Run 1 — 100% — 4,824/4,824 docs — 2s — 5m 53s
Run 1 took 5m 53s
**************************
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>**************************
* Update Script Finished *
**************************
</code></pre><ul>
</code></pre></div><ul>
<li>If I run it again it finds the same 4,824 docs and processes them&hellip;
<ul>
<li>I asked Atmire for feedback on this: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839</a></li>
@ -796,8 +796,8 @@ Run 1 took 5m 53s
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">2021-03-29 08:55:40,073 INFO org.apache.solr.core.SolrCore @ [search] webapp=/solr path=/select params={q=Gender+mainstreaming+in+local+potato+seed+system+in+Georgia&amp;fl=handle,search.resourcetype,search.resourceid,search.uniqueid&amp;start=0&amp;fq=NOT(withdrawn:true)&amp;fq=NOT(discoverable:false)&amp;fq=-location:l5308ea39-7c65-401b-890b-c2b93dad649a&amp;wt=javabin&amp;version=2} hits=143 status=0 QTime=0
</code></pre><ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">2021-03-29 08:55:40,073 INFO org.apache.solr.core.SolrCore @ [search] webapp=/solr path=/select params={q=Gender+mainstreaming+in+local+potato+seed+system+in+Georgia&amp;fl=handle,search.resourcetype,search.resourceid,search.uniqueid&amp;start=0&amp;fq=NOT(withdrawn:true)&amp;fq=NOT(discoverable:false)&amp;fq=-location:l5308ea39-7c65-401b-890b-c2b93dad649a&amp;wt=javabin&amp;version=2} hits=143 status=0 QTime=0
</code></pre></div><ul>
<li>But the item mapper only displays ten items, with no pagination
<ul>
<li>There is no way to search by handle or ID</li>
@ -845,9 +845,9 @@ r <span style="color:#f92672">=</span> requests<span style="color:#f92672">.</sp
</code></pre></div><ul>
<li>I exported a list of all our ISSNs from CGSpace:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=253) to /tmp/2021-03-31-issns.csv;
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=253) to /tmp/2021-03-31-issns.csv;
COPY 3081
</code></pre><ul>
</code></pre></div><ul>
<li>I wrote a script to check the ISSNs against Crossref&rsquo;s API: <code>crossref-issn-lookup.py</code>
<ul>
<li>I suspect Crossref might have better data actually&hellip;</li>