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Discuss some OpenRXV issues with Abdullah from CodeObia
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He’s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API
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Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies
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Discuss some OpenRXV issues with Abdullah from CodeObia
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He’s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API
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Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2021-03-01">2021-03-01</h2>
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<ul>
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<li>Discuss some OpenRXV issues with Abdullah from CodeObia
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<ul>
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<li>He’s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
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<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-03-02">2021-03-02</h2>
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<ul>
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<li>I fixed three build and runtime issues in OpenRXV:
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<ul>
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<li><a href="https://github.com/ilri/OpenRXV/pull/80">fix highcharts-angular and ngx-tour-core build</a></li>
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<li><a href="https://github.com/ilri/OpenRXV/pull/82">frontend/package.json: Pin @types/ramda at 0.27.34</a></li>
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</ul>
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</li>
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<li>Then I merged a few fixes that Abdullah had worked on last week</li>
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</ul>
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<h2 id="2021-03-03">2021-03-03</h2>
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<ul>
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<li>I <a href="https://github.com/ilri/OpenRXV/issues/83">fixed another frontend build warning on OpenRXV</a></li>
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<li>Then I <a href="https://github.com/ilri/OpenRXV/pull/84">updated the frontend container to use Node.js 12 and Ubuntu 20.04</a></li>
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<li>Also, I <a href="https://github.com/ilri/OpenRXV/pull/85">added a GitHub Actions workflow to build the frontend</a></li>
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<li>I did some testing of Abdullah’s patch for the values mapping search on OpenRXV
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<ul>
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<li>It still doesn’t work with multi-word values, so I recorded a video with wf-recorder and uploaded it to <a href="https://github.com/ilri/OpenRXV/issues/43">the issue</a> for him to investigate</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-03-04">2021-03-04</h2>
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<ul>
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<li>Peter is having issues with the workflow since yesterday
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<ul>
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<li>I looked at the Munin stats and see a high number of database locks since yesterday</li>
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</ul>
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</li>
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</ul>
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<p><img src="/cgspace-notes/2021/03/postgres_locks_ALL-week.png" alt="PostgreSQL locks week">
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<img src="/cgspace-notes/2021/03/postgres_connections_cgspace-week.png" alt="PostgreSQL connections week"></p>
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<ul>
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<li>I looked at the number of connections in PostgreSQL and it’s definitely high again:</li>
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</ul>
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<pre><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
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1020
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</code></pre><ul>
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<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>
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<li>Abenet asked me to add a new ORCID for ILRI staff member Zoe Campbell</li>
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<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>
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</ul>
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<pre><code class="language-console" data-lang="console">$ cat 2021-03-04-add-zoe-campbell-orcid.csv
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dc.contributor.author,cg.creator.identifier
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"Campbell, Zoë","Zoe Campbell: 0000-0002-4759-9976"
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"Campbell, Zoe A.","Zoe Campbell: 0000-0002-4759-9976"
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$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p 'fuuu'
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</code></pre><ul>
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<li>I still need to do cleanup on the journal articles metadata
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<ul>
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<li>Peter sent me some cleanups but I can’t use them in the search/replace format he gave</li>
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<li>I think it’s better to export the metadata values with IDs and import cleaned up ones as CSV</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">localhost/dspace63= > \COPY (SELECT dspace_object_id AS id, text_value as "cg.journal" 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;
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COPY 32087
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</code></pre><ul>
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<li>I used OpenRefine to remove all journal values that didn’t have one of these values: ; ( )
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<ul>
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<li>Then I cloned the <code>cg.journal</code> field to <code>cg.volume</code> and <code>cg.issue</code></li>
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<li>I used some GREL expressions like these to extract the journal name, volume, and issue:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">value.partition(';')[0].trim() # to get journal names
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value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,"$1") # to get journal volumes
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value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,"$1") # to get journal issues
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</code></pre><ul>
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<li>Then I uploaded the changes to CGSpace using <code>dspace metadata-import</code></li>
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<li>Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
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<ul>
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<li>The error was “Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e …”</li>
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<li>I searched the DSpace issue tracker and found several issues reporting this:
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<ul>
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<li><a href="https://jira.lyrasis.org/browse/DS-3985">DS-3985 Delete item fails</a></li>
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<li><a href="https://jira.lyrasis.org/browse/DS-4004">DS-4004 Authorization denied Exception when trying to delete permanently an item, collection or community as a non-Admin user</a></li>
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<li><a href="https://jira.lyrasis.org/browse/DS-4297">DS-4297 Authorization error when trying to delete item by submitter/administrator</a></li>
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</ul>
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</li>
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<li>The issue is apparently with non-admin users who are in the admin and submit groups of the owning collection…</li>
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<li>In this case the item was uploaded to the CCAFS Reports collection, and Margarita is a non-admin user who is a member of the collection’s admin and submit groups, exactly as the issue described</li>
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<li>I added a comment about our issue to <a href="https://jira.lyrasis.org/browse/DS-4297">DS-4297</a></li>
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</ul>
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</li>
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<li>Yesterday Abenet added me to a WLE collection approver/editer steps so we can try to figure out why Niroshini is having issues adding metadata to Udana’s submissions
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<ul>
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<li>I edited Udana’s submission to CGSpace:
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<ul>
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<li>corrected the title</li>
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<li>added language English</li>
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<li>changed the link to the external item page instead of PDF</li>
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<li>added SDGs from the external item page</li>
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<li>added AGROVOC subjects from the external item page</li>
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<li>added pagination (extent)</li>
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<li>changed the license to “other” because CC-BY-NC-ND is not printed anywhere in the PDF or external item page</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-03-05">2021-03-05</h2>
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<ul>
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<li>I migrated the Docker bind mount for the AReS Elasticsearch container to a Docker volume:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ docker-compose -f docker/docker-compose.yml down
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$ docker volume create docker_esData_7
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$ docker container create --name es_dummy -v docker_esData_7:/usr/share/elasticsearch/data:rw elasticsearch:7.6.2
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$ docker cp docker/esData_7/nodes es_dummy:/usr/share/elasticsearch/data
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$ docker rm es_dummy
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# edit docker/docker-compose.yml to switch from bind mount to volume
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$ docker-compose -f docker/docker-compose.yml up -d
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</code></pre><ul>
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<li>The trick is that when you create a volume like “myvolume” from a <code>docker-compose.yml</code> file, Docker will create it with the name “docker_myvolume”
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<ul>
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<li>If you create it manually on the command line with <code>docker volume create myvolume</code> then the name is literally “myvolume”</li>
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</ul>
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</li>
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<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>
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<li>Delete the <code>openrxv-items-temp</code> index to test a fresh harvesting:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
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</code></pre><h2 id="2021-03-05-1">2021-03-05</h2>
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<ul>
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<li>Check the results of the AReS harvesting from last night:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
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{
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"count" : 101761,
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"_shards" : {
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"total" : 1,
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"successful" : 1,
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"skipped" : 0,
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"failed" : 0
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}
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}
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</code></pre><ul>
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<li>Set the current items index to read only and make a backup:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d' {"settings": {"index.blocks.write":true}}'
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$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-03-05
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</code></pre><ul>
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<li>Delete the current items index and clone the temp one to it:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items'
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$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
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$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items
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</code></pre><ul>
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<li>Then delete the temp and backup:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
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{"acknowledged":true}%
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$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-03-05'
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</code></pre><ul>
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<li>I made some pull requests to OpenRXV:
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<ul>
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<li><a href="https://github.com/ilri/OpenRXV/pull/86">docker/docker-compose.yml: Use docker volumes</a></li>
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<li><a href="https://github.com/ilri/OpenRXV/pull/87">docker/docker-compose.yml: Pin Redis to version 5</a></li>
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</ul>
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</li>
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<li>I deployed the latest changes from the last few days on AReS production</li>
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</ul>
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<h2 id="2021-03-07">2021-03-07</h2>
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<ul>
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<li>I realized there is something wrong with the Elasticsearch indexes on AReS
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<ul>
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<li>On a new test environment I see <code>openrxv-items</code> is correctly an alias of <code>openrxv-items-final</code>:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
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...
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"openrxv-items-final": {
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"aliases": {
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"openrxv-items": {}
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}
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},
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</code></pre><ul>
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<li>But on AReS production <code>openrxv-items</code> has somehow become an index:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
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...
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"openrxv-items": {
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"aliases": {}
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},
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"openrxv-items-final": {
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"aliases": {}
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},
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"openrxv-items-temp": {
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"aliases": {}
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},
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</code></pre><ul>
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<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>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
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$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-03-07
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$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
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$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-final
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$ curl -XDELETE 'http://localhost:9200/openrxv-items'
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$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
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</code></pre><ul>
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<li>Delete backups and remove read-only mode on <code>openrxv-items</code>:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-03-07'
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$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
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</code></pre><ul>
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<li>Linode sent alerts about the CPU usage on CGSpace yesterday and the day before
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<ul>
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<li>Looking in the logs I see a few IPs making heavy usage on the REST API and XMLUI:</li>
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</ul>
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</li>
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</ul>
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<pre><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 -
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</code></pre><ul>
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<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>
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</ul>
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<pre><code class="language-console" data-lang="console"># zgrep '143.233.242.132' /var/log/nginx/access.log.1 | grep -c Delphi
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6237
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# zgrep '143.233.242.132' /var/log/nginx/access.log.1 | grep -c -v Delphi
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6418
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</code></pre><ul>
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<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 “normal” user agent
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<ul>
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<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>
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<li>I will add this IP to the list of bots in nginx and purge it from Solr with my <code>check-spider-ip-hits.sh</code> script</li>
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</ul>
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</li>
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<li>I made a few changes to OpenRXV:
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<ul>
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|
<li><a href="https://github.com/ilri/OpenRXV/issues/89">Migrated away from links to use networks</a></li>
|
|
<li><a href="https://github.com/ilri/OpenRXV/issues/68">Converted the backend container to use a custom image that includes <code>unoconv</code></a> so we don’t have to manually install it anymore</li>
|
|
</ul>
|
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</li>
|
|
</ul>
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|
<h2 id="2021-03-08">2021-03-08</h2>
|
|
<ul>
|
|
<li>I approved the WLE item that I edited last week, and all the metadata is there: <a href="https://hdl.handle.net/10568/111810">https://hdl.handle.net/10568/111810</a>
|
|
<ul>
|
|
<li>So I’m not sure what Niroshini’s issue with metadata is…</li>
|
|
</ul>
|
|
</li>
|
|
<li>Peter sent a message yesterday saying that his item finally got committed
|
|
<ul>
|
|
<li>I looked at the Munin graphs and there was a MASSIVE spike in database activity two days ago, and now database locks are back down to normal levels (from 1000+):</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><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
|
|
13
|
|
</code></pre><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>
|
|
<ul>
|
|
<li>After that the connections and locks started going up, peaking on 2021-03-06:</li>
|
|
</ul>
|
|
<p><img src="/cgspace-notes/2021/03/postgres_locks_ALL-week.png" alt="PostgreSQL locks week">
|
|
<img src="/cgspace-notes/2021/03/postgres_connections_ALL-week.png" alt="PostgreSQL connections week"></p>
|
|
<ul>
|
|
<li>I sent another message to Atmire to ask if they have time to look into this</li>
|
|
<li>CIFOR is pressuring me to upload the batch items from last week
|
|
<ul>
|
|
<li>Vika sent me a final file with some duplicates that Peter identified removed</li>
|
|
<li>I extracted and re-applied my basic corrections from last week in OpenRefine, then ran the items through <code>csv-metadata-quality</code> checker and uploaded them to CGSpace</li>
|
|
<li>In total there are 1,088 items</li>
|
|
</ul>
|
|
</li>
|
|
<li>Udana from IWMI emailed to ask about CGSpace thumbnails</li>
|
|
<li>Udana from IWMI emailed to ask about an item uploaded recently that does not appear in AReS
|
|
<ul>
|
|
<li><a href="https://hdl.handle.net/10568/111794">The item</a> was added to the archive on 2021-03-05, and I last harvested on 2021-03-06, so this might be an issue of a missing item</li>
|
|
</ul>
|
|
</li>
|
|
<li>Abenet got a quote from Atmire to buy 125 credits for 3750€</li>
|
|
<li>Maria at Bioversity sent some feedback about duplicate items on AReS</li>
|
|
<li>I’m wondering if the issue of the <code>openrxv-items-final</code> index not getting cleared after a successful harvest (which results in having 200,000, then 300,000, etc items) has to do with the alias issue I fixed yesterday
|
|
<ul>
|
|
<li>I will start a fresh harvest on AReS without now to check, but first back up the current index just in case:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
|
|
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-2021-03-08
|
|
# start harvesting on AReS
|
|
</code></pre><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>
|
|
<ul>
|
|
<li>The harvesting on AReS finished last night and everything worked as expected, with no manual intervention
|
|
<ul>
|
|
<li>This means that <a href="https://github.com/ilri/OpenRXV/issues/64">the issue</a> we were facing for a few months was due to the <code>openrxv-items</code> index being deleted and re-created as a standalone index instead of an alias of <code>openrxv-items-final</code></li>
|
|
</ul>
|
|
</li>
|
|
<li>Talk to Moayad about OpenRXV development
|
|
<ul>
|
|
<li>We realized that the missing/duplicate items issue is probably due to the long harvesting time on the REST API, as the time between starting the harvesting on page 0 and finishing the harvesting on page 900 (in the CGSpace example), some items will have been added to the repository, which causes the pages to shift</li>
|
|
<li>I proposed a solution in the <a href="https://github.com/ilri/OpenRXV/issues/67">GitHub issue</a>, where we consult the site’s XML sitemap after harvesting to see if we missed any items, and then we harvest them individually</li>
|
|
</ul>
|
|
</li>
|
|
<li>Peter sent me a list of 356 DOIs from Altmetric that don’t have our Handles, so we need to Tweet them
|
|
<ul>
|
|
<li>I used my <code>doi-to-handle.py</code> script to generate a list of handles and titles for him:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><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>
|
|
<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>
|
|
<li>I filed <a href="https://github.com/AgriculturalSemantics/cg-core/issues/39">an issue</a> on the cg-core project to ask colleagues for ideas</li>
|
|
</ul>
|
|
</li>
|
|
<li>Peter said he doesn’t see “Source Code” or “Software” 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><code class="language-console" data-lang="console">$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
|
|
|
real 318m20.485s
|
|
user 215m15.196s
|
|
sys 2m51.529s
|
|
</code></pre><ul>
|
|
<li>Now I see ten items for “Source Code” in the facets…</li>
|
|
</ul>
|
|
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</article>
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
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|
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<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
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<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
|
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|
|
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
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|
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<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
|
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<h4>Links</h4>
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<ol class="list-unstyled">
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|
|
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
|
|
|
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
|
|
|
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
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|
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</ol>
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</section>
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