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Add notes for 2021-05-25

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Alan Orth 2021-05-25 21:20:22 +03:00
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101
content/posts/2021-05.md
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@ -378,4 +378,105 @@ $ ./ilri/add-orcid-identifiers-csv.py -i /tmp/2021-05-18-add-orcids.csv -db dspa
- This included the IWMI changes, so I also migrated the `cg.subject.iwmi` metadata to `dcterms.subject` and deleted the subject term
- Then I started a full Discovery reindex
## 2021-05-19
- I realized that I need to lower case the IWMI subjects that I just moved to AGROVOC because they were probably mostly uppercase
- To my surprise I checked `dcterms.subject` has 47,000 metadata fields that are upper or mixed case!
```console
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=187 AND text_value ~ '[[:upper:]]';
UPDATE 47405
```
- That's interesting because we lowercased them all a few months ago, so these must all be new... wow
- We have 405,000 total AGROVOC terms, with 20,600 of them being unique
- I will have to start another Discovery re-indexing to pick up these new changes
## 2021-05-20
- Export the top 5,000 AGROVOC terms to validate them:
```console
localhost/dspace63= > \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 187 GROUP BY text_value ORDER BY count DESC LIMIT 5000) to /tmp/2021-05-20-agrovoc.csv WITH CSV HEADER;
COPY 5000
$ csvcut -c 1 /tmp/2021-05-20-agrovoc.csv| sed 1d > /tmp/2021-05-20-agrovoc.txt
$ ./ilri/agrovoc-lookup.py -i /tmp/2021-05-20-agrovoc.txt -o /tmp/2021-05-20-agrovoc-results.csv
$ csvgrep -c "number of matches" -m 0 /tmp/2021-05-20-agrovoc-results.csv > /tmp/2021-05-20-agrovoc-rejected.csv
```
- Meeting with Medha and Pythagoras about the FAIR Workflow tool
- Discussed the need for such a tool, other tools being developed, etc
- I stressed the important of controlled vocabularies
- No real outcome, except to keep us posted and let us know if they need help testing on DSpace
- Meeting with Hector Tobon to discuss issues with CLARISA
- They pushed back a bit, saying they were more focused on the needs of the CG
- They are not against the idea of aligning closer to ROR, but lack the man power
- They pointed out that their countries come directly from the [ISO 3166 online browsing platform on the ISO website](https://www.iso.org/iso-3166-country-codes.html)
- Indeed the text value for Russia is "Russian Federation (the)" there... I find that strange
- I filed [an issue](https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/33) on the iso-codes GitLab repository
## 2021-05-24
- Add ORCID identifiers for missing ILRI authors and tag 550 others based on a few authors I noticed that were missing them:
```console
$ cat 2021-05-24-add-orcids.csv
dc.contributor.author,cg.creator.identifier
"Patel, Ekta","Ekta Patel: 0000-0001-9400-6988"
"Dessie, Tadelle","Tadelle Dessie: 0000-0002-1630-0417"
"Tadelle, D.","Tadelle Dessie: 0000-0002-1630-0417"
"Dione, Michel M.","Michel Dione: 0000-0001-7812-5776"
"Kiara, Henry K.","Henry Kiara: 0000-0001-9578-1636"
"Naessens, Jan","Jan Naessens: 0000-0002-7075-9915"
"Steinaa, Lucilla","Lucilla Steinaa: 0000-0003-3691-3971"
"Wieland, Barbara","Barbara Wieland: 0000-0003-4020-9186"
"Grace, Delia","Delia Grace: 0000-0002-0195-9489"
"Rao, Idupulapati M.","Idupulapati M. Rao: 0000-0002-8381-9358"
"Cardoso Arango, Juan Andrés","Juan Andrés Cardoso Arango: 0000-0002-0252-4655"
$ ./ilri/add-orcid-identifiers-csv.py -i 2021-05-24-add-orcids.csv -db dspace -u dspace -p 'fuuu'
```
- A few days ago I took a backup of the Elasticsearch indexes on AReS using elasticdump:
```console
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --type=data --limit=1000
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
```
- The indexes look OK so I started a harvesting on AReS
## 2021-05-25
- The AReS harvest got messed up somehow, as I see the number of items in the indexes are the same as before the harvesting:
```console
$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
yellow open openrxv-items-temp o3ijJLcyTtGMOPeWpAJiVA 1 1 104373 106455 491.5mb 491.5mb
yellow open openrxv-items-final soEzAnp3TDClIGZbmVyEIw 1 1 953 0 2.3mb 2.3mb
```
- Update all docker images on the AReS server (linode20):
```console
$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
$ docker-compose -f docker/docker-compose.yml down
$ docker-compose -f docker/docker-compose.yml build
```
- Then run all system updates on the server and reboot it
- Oh crap, I deleted everything on AReS and restored the backup and the total items are now 104317... so it was actually correct before!
- For reference, this is how I re-created everything:
```console
curl -XDELETE 'http://localhost:9200/openrxv-items-final'
curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
curl -XPUT 'http://localhost:9200/openrxv-items-final'
curl -XPUT 'http://localhost:9200/openrxv-items-temp'
curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-final --type=data --limit=1000
```
- I will just start a new harvest... sigh
<!-- vim: set sw=2 ts=2: -->

7
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@ -32,7 +32,7 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-02/" />
<meta property="article:published_time" content="2021-02-01T10:13:54+02:00" />
<meta property="article:modified_time" content="2021-03-04T22:46:05+02:00" />
<meta property="article:modified_time" content="2021-05-18T23:21:39+03:00" />
@ -70,9 +70,9 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
"@type": "BlogPosting",
"headline": "February, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-02/",
"wordCount": "4170",
"wordCount": "4143",
"datePublished": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-04T22:46:05+02:00",
"dateModified": "2021-05-18T23:21:39+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -233,7 +233,6 @@ java.lang.NullPointerException
<li>Communicate more with CodeObia about some fixes for OpenRXV</li>
<li>Maria Garruccio sent me some new ORCID iDs for Bioversity authors, as well as a correction for Stefan Burkart&rsquo;s iD</li>
<li>I saved the new ones to a text file, combined them with the others, extracted the ORCID iDs themselves, and updated the names using <code>resolve-orcids.py</code>:</li>
<li>Then for the rest, I saved them to a text file, combined them with the others, extracted the ORCID iDs themselves, and updated the names using <code>resolve-orcids.py</code>:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcid-ids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq &gt; /tmp/2021-02-02-combined-orcids.txt
$ ./ilri/resolve-orcids.py -i /tmp/2021-02-02-combined-orcids.txt -o /tmp/2021-02-02-combined-orcid-names.txt

145
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@ -20,7 +20,7 @@ I will add the RI/1.0 pattern to our DSpace agents overload and purge them from
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-05/" />
<meta property="article:published_time" content="2021-05-02T09:50:54+03:00" />
<meta property="article:modified_time" content="2021-05-16T17:11:48+03:00" />
<meta property="article:modified_time" content="2021-05-18T23:21:39+03:00" />
@ -46,9 +46,9 @@ I will add the RI/1.0 pattern to our DSpace agents overload and purge them from
"@type": "BlogPosting",
"headline": "May, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-05/",
"wordCount": "2245",
"wordCount": "3089",
"datePublished": "2021-05-02T09:50:54+03:00",
"dateModified": "2021-05-16T17:11:48+03:00",
"dateModified": "2021-05-18T23:21:39+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -456,6 +456,145 @@ line 3659 column 23 - Warning: unescaped &amp; or unknown entity &quot;&amp;WA_E
</code></pre><ul>
<li>After testing whether this escaped value worked during submission, I created and merged a pull request to <code>6_x-prod</code> (<a href="https://github.com/ilri/DSpace/pull/468">#468</a>)</li>
</ul>
<h2 id="2021-05-18">2021-05-18</h2>
<ul>
<li>Paola from the Alliance emailed me some new ORCID identifiers to add to CGSpace</li>
<li>I saved the new ones to a text file, combined them with the others, extracted the ORCID iDs themselves, and updated the names using <code>resolve-orcids.py</code>:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/new | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq &gt; /tmp/2021-05-18-combined.txt
$ ./ilri/resolve-orcids.py -i /tmp/2021-05-18-combined.txt -o /tmp/2021-05-18-combined-names.txt
</code></pre><ul>
<li>I sorted the names and added the XML formatting in vim, then ran it through tidy:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ tidy -xml -utf8 -m -iq -w 0 dspace/config/controlled-vocabularies/cg-creator-identifier.xml
</code></pre><ul>
<li>Tag fifty-five items from the Alliance&rsquo;s new authors with ORCID iDs using <code>add-orcid-identifiers-csv.py</code>:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ cat 2021-05-18-add-orcids.csv
dc.contributor.author,cg.creator.identifier
&quot;Urioste Daza, Sergio&quot;,Sergio Alejandro Urioste Daza: 0000-0002-3208-032X
&quot;Urioste, Sergio&quot;,Sergio Alejandro Urioste Daza: 0000-0002-3208-032X
&quot;Villegas, Daniel&quot;,Daniel M. Villegas: 0000-0001-6801-3332
&quot;Villegas, Daniel M.&quot;,Daniel M. Villegas: 0000-0001-6801-3332
&quot;Giles, James&quot;,James Giles: 0000-0003-1899-9206
&quot;Simbare, Alice&quot;,Alice Simbare: 0000-0003-2389-0969
&quot;Simbare, Alice&quot;,Alice Simbare: 0000-0003-2389-0969
&quot;Simbare, A.&quot;,Alice Simbare: 0000-0003-2389-0969
&quot;Dita Rodriguez, Miguel&quot;,Miguel Angel Dita Rodriguez: 0000-0002-0496-4267
&quot;Templer, Noel&quot;,Noel Templer: 0000-0002-3201-9043
&quot;Jalonen, R.&quot;,Riina Jalonen: 0000-0003-1669-9138
&quot;Jalonen, Riina&quot;,Riina Jalonen: 0000-0003-1669-9138
&quot;Izquierdo, Paulo&quot;,Paulo Izquierdo: 0000-0002-2153-0655
&quot;Reyes, Byron&quot;,Byron Reyes: 0000-0003-2672-9636
&quot;Reyes, Byron A.&quot;,Byron Reyes: 0000-0003-2672-9636
$ ./ilri/add-orcid-identifiers-csv.py -i /tmp/2021-05-18-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
</code></pre><ul>
<li>I deployed the latest <code>6_x-prod</code> branch on CGSpace, ran all system updates, and rebooted the server
<ul>
<li>This included the IWMI changes, so I also migrated the <code>cg.subject.iwmi</code> metadata to <code>dcterms.subject</code> and deleted the subject term</li>
<li>Then I started a full Discovery reindex</li>
</ul>
</li>
</ul>
<h2 id="2021-05-19">2021-05-19</h2>
<ul>
<li>I realized that I need to lower case the IWMI subjects that I just moved to AGROVOC because they were probably mostly uppercase
<ul>
<li>To my surprise I checked <code>dcterms.subject</code> has 47,000 metadata fields that are upper or mixed case!</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=187 AND text_value ~ '[[:upper:]]';
UPDATE 47405
</code></pre><ul>
<li>That&rsquo;s interesting because we lowercased them all a few months ago, so these must all be new&hellip; wow
<ul>
<li>We have 405,000 total AGROVOC terms, with 20,600 of them being unique</li>
<li>I will have to start another Discovery re-indexing to pick up these new changes</li>
</ul>
</li>
</ul>
<h2 id="2021-05-20">2021-05-20</h2>
<ul>
<li>Export the top 5,000 AGROVOC terms to validate them:</li>
</ul>
<pre><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 187 GROUP BY text_value ORDER BY count DESC LIMIT 5000) to /tmp/2021-05-20-agrovoc.csv WITH CSV HEADER;
COPY 5000
$ csvcut -c 1 /tmp/2021-05-20-agrovoc.csv| sed 1d &gt; /tmp/2021-05-20-agrovoc.txt
$ ./ilri/agrovoc-lookup.py -i /tmp/2021-05-20-agrovoc.txt -o /tmp/2021-05-20-agrovoc-results.csv
$ csvgrep -c &quot;number of matches&quot; -m 0 /tmp/2021-05-20-agrovoc-results.csv &gt; /tmp/2021-05-20-agrovoc-rejected.csv
</code></pre><ul>
<li>Meeting with Medha and Pythagoras about the FAIR Workflow tool
<ul>
<li>Discussed the need for such a tool, other tools being developed, etc</li>
<li>I stressed the important of controlled vocabularies</li>
<li>No real outcome, except to keep us posted and let us know if they need help testing on DSpace</li>
</ul>
</li>
<li>Meeting with Hector Tobon to discuss issues with CLARISA
<ul>
<li>They pushed back a bit, saying they were more focused on the needs of the CG</li>
<li>They are not against the idea of aligning closer to ROR, but lack the man power</li>
<li>They pointed out that their countries come directly from the <a href="https://www.iso.org/iso-3166-country-codes.html">ISO 3166 online browsing platform on the ISO website</a></li>
<li>Indeed the text value for Russia is &ldquo;Russian Federation (the)&rdquo; there&hellip; I find that strange</li>
<li>I filed <a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/33">an issue</a> on the iso-codes GitLab repository</li>
</ul>
</li>
</ul>
<h2 id="2021-05-24">2021-05-24</h2>
<ul>
<li>Add ORCID identifiers for missing ILRI authors and tag 550 others based on a few authors I noticed that were missing them:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ cat 2021-05-24-add-orcids.csv
dc.contributor.author,cg.creator.identifier
&quot;Patel, Ekta&quot;,&quot;Ekta Patel: 0000-0001-9400-6988&quot;
&quot;Dessie, Tadelle&quot;,&quot;Tadelle Dessie: 0000-0002-1630-0417&quot;
&quot;Tadelle, D.&quot;,&quot;Tadelle Dessie: 0000-0002-1630-0417&quot;
&quot;Dione, Michel M.&quot;,&quot;Michel Dione: 0000-0001-7812-5776&quot;
&quot;Kiara, Henry K.&quot;,&quot;Henry Kiara: 0000-0001-9578-1636&quot;
&quot;Naessens, Jan&quot;,&quot;Jan Naessens: 0000-0002-7075-9915&quot;
&quot;Steinaa, Lucilla&quot;,&quot;Lucilla Steinaa: 0000-0003-3691-3971&quot;
&quot;Wieland, Barbara&quot;,&quot;Barbara Wieland: 0000-0003-4020-9186&quot;
&quot;Grace, Delia&quot;,&quot;Delia Grace: 0000-0002-0195-9489&quot;
&quot;Rao, Idupulapati M.&quot;,&quot;Idupulapati M. Rao: 0000-0002-8381-9358&quot;
&quot;Cardoso Arango, Juan Andrés&quot;,&quot;Juan Andrés Cardoso Arango: 0000-0002-0252-4655&quot;
$ ./ilri/add-orcid-identifiers-csv.py -i 2021-05-24-add-orcids.csv -db dspace -u dspace -p 'fuuu'
</code></pre><ul>
<li>A few days ago I took a backup of the Elasticsearch indexes on AReS using elasticdump:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --type=data --limit=1000
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
</code></pre><ul>
<li>The indexes look OK so I started a harvesting on AReS</li>
</ul>
<h2 id="2021-05-25">2021-05-25</h2>
<ul>
<li>The AReS harvest got messed up somehow, as I see the number of items in the indexes are the same as before the harvesting:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
yellow open openrxv-items-temp o3ijJLcyTtGMOPeWpAJiVA 1 1 104373 106455 491.5mb 491.5mb
yellow open openrxv-items-final soEzAnp3TDClIGZbmVyEIw 1 1 953 0 2.3mb 2.3mb
</code></pre><ul>
<li>Update all docker images on the AReS server (linode20):</li>
</ul>
<pre><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
$ docker-compose -f docker/docker-compose.yml down
$ docker-compose -f docker/docker-compose.yml build
</code></pre><ul>
<li>Then run all system updates on the server and reboot it</li>
<li>Oh crap, I deleted everything on AReS and restored the backup and the total items are now 104317&hellip; so it was actually correct before!</li>
<li>For reference, this is how I re-created everything:</li>
</ul>
<pre><code class="language-console" data-lang="console">curl -XDELETE 'http://localhost:9200/openrxv-items-final'
curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
curl -XPUT 'http://localhost:9200/openrxv-items-final'
curl -XPUT 'http://localhost:9200/openrxv-items-temp'
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;}}]}'
elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-final --type=data --limit=1000
</code></pre><ul>
<li>I will just start a new harvest&hellip; sigh</li>
</ul>
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2021-05-16T17:11:48+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-05-16T17:11:48+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-05-16T17:11:48+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-05-16T17:11:48+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-05-16T17:11:48+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-05-16T17:11:48+03:00" />
<meta property="og:updated_time" content="2021-05-18T23:21:39+03:00" />

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