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Add notes for 2021-04-18

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Alan Orth 2021-04-18 10:07:54 +03:00
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@ -492,7 +492,6 @@ $ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-
$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
```
- Then I updated all Docker containers and rebooted the server (linode20) so that the correct indexes would be created again:
@ -611,4 +610,80 @@ $ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p 'fuuuuuuuu'
- I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
- According to my notes from [2020-10]({{< relref "2020-10.md" >}}) the account must be in the admin group in order to submit via the REST API
## 2021-04-18
- Update all containers on AReS (linode20):
```console
$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
```
- Then run all system updates and reboot the server
- I learned a new command for Elasticsearch:
```console
$ curl http://localhost:9200/_cat/indices
yellow open openrxv-values ChyhGwMDQpevJtlNWO1vcw 1 1 1579 0 537.6kb 537.6kb
yellow open openrxv-items-temp PhV5ieuxQsyftByvCxzSIw 1 1 103585 104372 482.7mb 482.7mb
yellow open openrxv-shared J_8cxIz6QL6XTRZct7UBBQ 1 1 127 0 115.7kb 115.7kb
yellow open openrxv-values-00001 jAoXTLR0R9mzivlDVbQaqA 1 1 3903 0 696.2kb 696.2kb
green open .kibana_task_manager_1 O1zgJ0YlQhKCFAwJZaNSIA 1 0 2 2 20.6kb 20.6kb
yellow open openrxv-users 1hWGXh9kS_S6YPxAaBN8ew 1 1 5 0 28.6kb 28.6kb
green open .apm-agent-configuration f3RAkSEBRGaxJZs3ePVxsA 1 0 0 0 283b 283b
yellow open openrxv-items-final sgk-s8O-RZKdcLRoWt3G8A 1 1 970 0 2.3mb 2.3mb
green open .kibana_1 HHPN7RD_T7qe0zDj4rauQw 1 0 25 7 36.8kb 36.8kb
yellow open users M0t2LaZhSm2NrF5xb64dnw 1 1 2 0 11.6kb 11.6kb
```
- Somehow the `openrxv-items-final` index only has a few items and the majority are in `openrxv-items-temp`, via the `openrxv-items` alias (which is in the temp index):
```console
$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'
{
"count" : 103585,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
```
- I found a cool tool to help with exporting and restoring Elasticsearch indexes:
```console
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
...
Sun, 18 Apr 2021 06:27:07 GMT | Total Writes: 103585
Sun, 18 Apr 2021 06:27:07 GMT | dump complete
```
- It took only two or three minutes to export everything...
- I did a test to restore the index:
```console
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-test --type=mapping
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-test --limit 1000 --type=data
```
- So that's pretty cool!
- I deleted the `openrxv-items-final` index and `openrxv-items-temp` indexes and then restored the mappings to `openrxv-items-final`, added the `openrxv-items` alias, and started restoring the data to `openrxv-items` with elasticdump:
```console
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
$ 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_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
```
- AReS seems to be working fine аfter that, so I created the `openrxv-items-temp` index and then started a fresh harvest on AReS Explorer:
```console
$ curl -X PUT "localhost:9200/openrxv-items-temp"
```
- Run system updates on CGSpace (linode18) and run the latest Ansible infrastructure playbook to update the DSpace Statistics API, PostgreSQL JDBC driver, etc, and then reboot the system
<!-- vim: set sw=2 ts=2: -->

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@ -24,7 +24,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-04/" />
<meta property="article:published_time" content="2021-04-01T09:50:54+03:00" />
<meta property="article:modified_time" content="2021-04-13T21:13:08+03:00" />
<meta property="article:modified_time" content="2021-04-15T16:27:06+03:00" />
@ -54,9 +54,9 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
"@type": "BlogPosting",
"headline": "April, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-04/",
"wordCount": "3137",
"wordCount": "3527",
"datePublished": "2021-04-01T09:50:54+03:00",
"dateModified": "2021-04-13T21:13:08+03:00",
"dateModified": "2021-04-15T16:27:06+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -613,7 +613,6 @@ $ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-
$ 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}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
</code></pre><ul>
<li>Then I updated all Docker containers and rebooted the server (linode20) so that the correct indexes would be created again:</li>
</ul>
@ -732,6 +731,68 @@ Total number of bot hits purged: 13159
</ul>
</li>
</ul>
<h2 id="2021-04-18">2021-04-18</h2>
<ul>
<li>Update all containers on AReS (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
</code></pre><ul>
<li>Then run all system updates and reboot the server</li>
<li>I learned a new command for Elasticsearch:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl http://localhost:9200/_cat/indices
yellow open openrxv-values ChyhGwMDQpevJtlNWO1vcw 1 1 1579 0 537.6kb 537.6kb
yellow open openrxv-items-temp PhV5ieuxQsyftByvCxzSIw 1 1 103585 104372 482.7mb 482.7mb
yellow open openrxv-shared J_8cxIz6QL6XTRZct7UBBQ 1 1 127 0 115.7kb 115.7kb
yellow open openrxv-values-00001 jAoXTLR0R9mzivlDVbQaqA 1 1 3903 0 696.2kb 696.2kb
green open .kibana_task_manager_1 O1zgJ0YlQhKCFAwJZaNSIA 1 0 2 2 20.6kb 20.6kb
yellow open openrxv-users 1hWGXh9kS_S6YPxAaBN8ew 1 1 5 0 28.6kb 28.6kb
green open .apm-agent-configuration f3RAkSEBRGaxJZs3ePVxsA 1 0 0 0 283b 283b
yellow open openrxv-items-final sgk-s8O-RZKdcLRoWt3G8A 1 1 970 0 2.3mb 2.3mb
green open .kibana_1 HHPN7RD_T7qe0zDj4rauQw 1 0 25 7 36.8kb 36.8kb
yellow open users M0t2LaZhSm2NrF5xb64dnw 1 1 2 0 11.6kb 11.6kb
</code></pre><ul>
<li>Somehow the <code>openrxv-items-final</code> index only has a few items and the majority are in <code>openrxv-items-temp</code>, via the <code>openrxv-items</code> alias (which is in the temp index):</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
{
&quot;count&quot; : 103585,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
</code></pre><ul>
<li>I found a cool tool to help with exporting and restoring Elasticsearch indexes:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
...
Sun, 18 Apr 2021 06:27:07 GMT | Total Writes: 103585
Sun, 18 Apr 2021 06:27:07 GMT | dump complete
</code></pre><ul>
<li>It took only two or three minutes to export everything&hellip;</li>
<li>I did a test to restore the index:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-test --type=mapping
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-test --limit 1000 --type=data
</code></pre><ul>
<li>So that&rsquo;s pretty cool!</li>
<li>I deleted the <code>openrxv-items-final</code> index and <code>openrxv-items-temp</code> indexes and then restored the mappings to <code>openrxv-items-final</code>, added the <code>openrxv-items</code> alias, and started restoring the data to <code>openrxv-items</code> with elasticdump:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
$ 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_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
</code></pre><ul>
<li>AReS seems to be working fine аfter that, so I created the <code>openrxv-items-temp</code> index and then started a fresh harvest on AReS Explorer:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-temp&quot;
</code></pre><ul>
<li>Run system updates on CGSpace (linode18) and run the latest Ansible infrastructure playbook to update the DSpace Statistics API, PostgreSQL JDBC driver, etc, and then reboot the system</li>
</ul>
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</url><url>
<loc>https://alanorth.github.io/cgspace-notes/2021-03/</loc>
<lastmod>2021-04-13T21:13:08+03:00</lastmod>