Update notes for 2020-12-14

This commit is contained in:
Alan Orth 2020-12-14 19:49:25 +02:00
parent 20f00d1279
commit 403fa49d46
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
23 changed files with 264 additions and 28 deletions

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@ -241,4 +241,114 @@ $ curl -XDELETE http://localhost:9200/openrxv-items-final
$ curl -XDELETE http://localhost:9200/openrxv-items-temp $ curl -XDELETE http://localhost:9200/openrxv-items-temp
``` ```
- Peter asked me for a list of all submitters and approvers that were active recently on CGSpace
- I can probably extract that from the `dc.description.provenance` field, for example any that contains a 2020 date:
```console
localhost/dspace63= > SELECT * FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-[0-9]{2}-*';
```
## 2020-12-14
- The re-harvesting finished last night on AReS but there are no records in the `openrxv-items-final` index
- Strangely, there are 99,000 items in the temp index:
```console
$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*' | json_pp
{
"count" : 99992,
"_shards" : {
"skipped" : 0,
"total" : 1,
"failed" : 0,
"successful" : 1
}
}
```
- I'm going to try to [clone](https://www.elastic.co/guide/en/elasticsearch/reference/master/indices-clone-index.html) the temp index to the final one...
- First, set the `openrxv-items-temp` index to block writes (read only) and then clone it to `openrxv-items-final`:
```console
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final"}
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
```
- Now I see that the `openrxv-items-final` index has items, but there are still none in AReS Explorer UI!
```console
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
{
"count" : 99992,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
```
- The api logs show this from last night after the harvesting:
```console
[Nest] 92 - 12/13/2020, 1:58:52 PM [HarvesterService] Starting Harvest
[Nest] 92 - 12/13/2020, 10:50:20 PM [FetchConsumer] OnGlobalQueueDrained
[Nest] 92 - 12/13/2020, 11:00:20 PM [PluginsConsumer] OnGlobalQueueDrained
[Nest] 92 - 12/13/2020, 11:00:20 PM [HarvesterService] reindex function is called
(node:92) UnhandledPromiseRejectionWarning: ResponseError: index_not_found_exception
at IncomingMessage.<anonymous> (/backend/node_modules/@elastic/elasticsearch/lib/Transport.js:232:25)
at IncomingMessage.emit (events.js:326:22)
at endReadableNT (_stream_readable.js:1223:12)
at processTicksAndRejections (internal/process/task_queues.js:84:21)
```
- But I'm not sure why the frontend doesn't show any data despite there being documents in the index...
- I talked to Moayad and he reminded me that OpenRXV uses an alias to point to temp and final indexes, but the UI actually uses the `openrxv-items` index
- I cloned the `openrxv-items-final` index to `openrxv-items` index and now I see items in the explorer UI
- The PDF report was broken and I looked in the API logs and saw this:
```console
(node:94) UnhandledPromiseRejectionWarning: Error: Error: Could not find soffice binary
at ExportService.downloadFile (/backend/dist/export/services/export/export.service.js:51:19)
at processTicksAndRejections (internal/process/task_queues.js:97:5)
```
- I installed `unoconv` in the backend api container and now it works... but I wonder why this changed...
- Skype with Abenet and Peter to discuss AReS that will be shown to ILRI scientists this week
- Peter noticed that [this item](https://hdl.handle.net/10568/110133) from the [ILRI policy and research briefs](https://cgspace.cgiar.org/handle/10568/24450) collection is missing in AReS, despite it being added one month ago in CGSpace and me harvesting on AReS last night
- The item appears fine in the REST API when I check the items in that collection
- Peter also noticed that [this item](https://hdl.handle.net/10568/110447) appears twice in AReS
- The item is _not_ duplicated on CGSpace or in the REST API
- We noticed that there are 136 items in the ILRI policy and research briefs collection according to AReS, yet on CGSpace there are only 132
- This is confirmed in the REST API (using [query-json](https://github.com/davesnx/query-json)):
```
$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&limit=100&offset=0' | json_pp > /tmp/policy1.json
$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&limit=100&offset=100' | json_pp > /tmp/policy2.json
$ query-json '.items | length' /tmp/policy1.json
100
$ query-json '.items | length' /tmp/policy2.json
32
```
- I realized that the issue of missing/duplicate items in AReS might be because of this [REST API bug that causes /items to return items in non-deterministic order](https://jira.lyrasis.org/browse/DS-3849)
- I decided to cherry-pick the following two patches from DSpace 6.4 into our `6_x-prod` (6.3) branch:
- High CPU usage when calling the collection_id/items REST endpoint
- Jira: https://jira.lyrasis.org/browse/DS-4342
- c2e6719fa763e291b81b2d61da2f8c758fe38ff3
- REST API items resource returns items in non-deterministic order
- Jira: https://jira.lyrasis.org/browse/DS-3849
- 2a2ea0cb5d03e6da9355a2eff12aad667e465433
- After deploying the REST API fixes I decided to harvest from AReS again to see if the missing and duplicate items get fixed
- I made a backup of the current `openrxv-items-temp` index just in case:
```console
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-2020-12-14
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
```
<!-- vim: set sw=2 ts=2: --> <!-- vim: set sw=2 ts=2: -->

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@ -20,7 +20,7 @@ I started processing those (about 411,000 records):
<meta property="og:type" content="article" /> <meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-12/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-12/" />
<meta property="article:published_time" content="2020-12-01T11:32:54+02:00" /> <meta property="article:published_time" content="2020-12-01T11:32:54+02:00" />
<meta property="article:modified_time" content="2020-12-10T23:43:09+02:00" /> <meta property="article:modified_time" content="2020-12-13T16:16:10+02:00" />
@ -46,9 +46,9 @@ I started processing those (about 411,000 records):
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "December, 2020", "headline": "December, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-12/", "url": "https://alanorth.github.io/cgspace-notes/2020-12/",
"wordCount": "1378", "wordCount": "2037",
"datePublished": "2020-12-01T11:32:54+02:00", "datePublished": "2020-12-01T11:32:54+02:00",
"dateModified": "2020-12-10T23:43:09+02:00", "dateModified": "2020-12-13T16:16:10+02:00",
"author": { "author": {
"@type": "Person", "@type": "Person",
"name": "Alan Orth" "name": "Alan Orth"
@ -364,6 +364,132 @@ Caused by: org.apache.http.TruncatedChunkException: Truncated chunk ( expected s
</ul> </ul>
<pre><code>$ curl -XDELETE http://localhost:9200/openrxv-items-final <pre><code>$ curl -XDELETE http://localhost:9200/openrxv-items-final
$ curl -XDELETE http://localhost:9200/openrxv-items-temp $ curl -XDELETE http://localhost:9200/openrxv-items-temp
</code></pre><ul>
<li>Peter asked me for a list of all submitters and approvers that were active recently on CGSpace
<ul>
<li>I can probably extract that from the <code>dc.description.provenance</code> field, for example any that contains a 2020 date:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">localhost/dspace63= &gt; SELECT * FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-[0-9]{2}-*';
</code></pre><h2 id="2020-12-14">2020-12-14</h2>
<ul>
<li>The re-harvesting finished last night on AReS but there are no records in the <code>openrxv-items-final</code> index
<ul>
<li>Strangely, there are 99,000 items in the temp index:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*' | json_pp
{
&quot;count&quot; : 99992,
&quot;_shards&quot; : {
&quot;skipped&quot; : 0,
&quot;total&quot; : 1,
&quot;failed&quot; : 0,
&quot;successful&quot; : 1
}
}
</code></pre><ul>
<li>I&rsquo;m going to try to <a href="https://www.elastic.co/guide/en/elasticsearch/reference/master/indices-clone-index.html">clone</a> the temp index to the final one&hellip;
<ul>
<li>First, set the <code>openrxv-items-temp</code> index to block writes (read only) and then clone it to <code>openrxv-items-final</code>:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
{&quot;acknowledged&quot;:true,&quot;shards_acknowledged&quot;:true,&quot;index&quot;:&quot;openrxv-items-final&quot;}
$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
</code></pre><ul>
<li>Now I see that the <code>openrxv-items-final</code> index has items, but there are still none in AReS Explorer UI!</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&amp;pretty'
{
&quot;count&quot; : 99992,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
</code></pre><ul>
<li>The api logs show this from last night after the harvesting:</li>
</ul>
<pre><code class="language-console" data-lang="console">[Nest] 92 - 12/13/2020, 1:58:52 PM [HarvesterService] Starting Harvest
[Nest] 92 - 12/13/2020, 10:50:20 PM [FetchConsumer] OnGlobalQueueDrained
[Nest] 92 - 12/13/2020, 11:00:20 PM [PluginsConsumer] OnGlobalQueueDrained
[Nest] 92 - 12/13/2020, 11:00:20 PM [HarvesterService] reindex function is called
(node:92) UnhandledPromiseRejectionWarning: ResponseError: index_not_found_exception
at IncomingMessage.&lt;anonymous&gt; (/backend/node_modules/@elastic/elasticsearch/lib/Transport.js:232:25)
at IncomingMessage.emit (events.js:326:22)
at endReadableNT (_stream_readable.js:1223:12)
at processTicksAndRejections (internal/process/task_queues.js:84:21)
</code></pre><ul>
<li>But I&rsquo;m not sure why the frontend doesn&rsquo;t show any data despite there being documents in the index&hellip;</li>
<li>I talked to Moayad and he reminded me that OpenRXV uses an alias to point to temp and final indexes, but the UI actually uses the <code>openrxv-items</code> index</li>
<li>I cloned the <code>openrxv-items-final</code> index to <code>openrxv-items</code> index and now I see items in the explorer UI</li>
<li>The PDF report was broken and I looked in the API logs and saw this:</li>
</ul>
<pre><code class="language-console" data-lang="console">(node:94) UnhandledPromiseRejectionWarning: Error: Error: Could not find soffice binary
at ExportService.downloadFile (/backend/dist/export/services/export/export.service.js:51:19)
at processTicksAndRejections (internal/process/task_queues.js:97:5)
</code></pre><ul>
<li>I installed <code>unoconv</code> in the backend api container and now it works&hellip; but I wonder why this changed&hellip;</li>
<li>Skype with Abenet and Peter to discuss AReS that will be shown to ILRI scientists this week
<ul>
<li>Peter noticed that <a href="https://hdl.handle.net/10568/110133">this item</a> from the <a href="https://cgspace.cgiar.org/handle/10568/24450">ILRI policy and research briefs</a> collection is missing in AReS, despite it being added one month ago in CGSpace and me harvesting on AReS last night
<ul>
<li>The item appears fine in the REST API when I check the items in that collection</li>
</ul>
</li>
<li>Peter also noticed that <a href="https://hdl.handle.net/10568/110447">this item</a> appears twice in AReS
<ul>
<li>The item is <em>not</em> duplicated on CGSpace or in the REST API</li>
</ul>
</li>
<li>We noticed that there are 136 items in the ILRI policy and research briefs collection according to AReS, yet on CGSpace there are only 132
<ul>
<li>This is confirmed in the REST API (using <a href="https://github.com/davesnx/query-json">query-json</a>):</li>
</ul>
</li>
</ul>
</li>
</ul>
<pre><code>$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&amp;limit=100&amp;offset=0' | json_pp &gt; /tmp/policy1.json
$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&amp;limit=100&amp;offset=100' | json_pp &gt; /tmp/policy2.json
$ query-json '.items | length' /tmp/policy1.json
100
$ query-json '.items | length' /tmp/policy2.json
32
</code></pre><ul>
<li>I realized that the issue of missing/duplicate items in AReS might be because of this <a href="https://jira.lyrasis.org/browse/DS-3849">REST API bug that causes /items to return items in non-deterministic order</a></li>
<li>I decided to cherry-pick the following two patches from DSpace 6.4 into our <code>6_x-prod</code> (6.3) branch:
<ul>
<li>High CPU usage when calling the collection_id/items REST endpoint
<ul>
<li>Jira: <a href="https://jira.lyrasis.org/browse/DS-4342">https://jira.lyrasis.org/browse/DS-4342</a></li>
<li>c2e6719fa763e291b81b2d61da2f8c758fe38ff3</li>
</ul>
</li>
<li>REST API items resource returns items in non-deterministic order
<ul>
<li>Jira: <a href="https://jira.lyrasis.org/browse/DS-3849">https://jira.lyrasis.org/browse/DS-3849</a></li>
<li>2a2ea0cb5d03e6da9355a2eff12aad667e465433</li>
</ul>
</li>
</ul>
</li>
<li>After deploying the REST API fixes I decided to harvest from AReS again to see if the missing and duplicate items get fixed
<ul>
<li>I made a backup of the current <code>openrxv-items-temp</code> index just in case:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-2020-12-14
$ curl -X PUT &quot;localhost:9200/openrxv-items-temp/_settings?pretty&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
</code></pre><!-- raw HTML omitted --> </code></pre><!-- raw HTML omitted -->

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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-12-10T23:43:09+02:00" /> <meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />

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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:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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