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Alan Orth 2020-12-16 09:54:40 +02:00
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content/posts/2020-12.md
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@ -389,8 +389,85 @@ dspace=# COMMIT;
```console
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m"
$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
real 265m11.224s
user 171m29.141s
sys 2m41.097s
```
- Udana sent a report that the WLE approver is experiencing the same issue Peter highlighted a few weeks ago: they are unable to save metadata edits in the workflow
- Yesterday Atmire responded about the owningComm and owningColl duplicates in Solr saying they didn't see any anymore...
- Indeed I spent a few minutes looking randomly and I didn't find any either...
- I did, however, see lots of duplicates in countryCode_search, countryCode_ngram, ip_search, ip_ngram, userAgent_search, userAgent_ngram, referrer_search, referrer_ngram fields
- I sent feedback to them
- On the database locking front we haven't had issues in over a week and the Munin graphs look normal:
![PostgreSQL connections all week](/cgspace-notes/2020/12/postgres_connections_ALL-week2.png)
![PostgreSQL locks all week](/cgspace-notes/2020/12/postgres_locks_ALL-week2.png)
- After the Discovery re-indexing finished on CGSpace I prepared to start re-harvesting AReS by making sure the `openrxv-items-temp` index was empty and that the backup index I made yesterday was still there:
```console
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
{
"acknowledged" : true
}
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
{
"count" : 0,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
$ curl -s 'http://localhost:9200/openrxv-items-2020-12-14/_count?q=*&pretty'
{
"count" : 99992,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
```
## 2020-12-16
- The harvesting on AReS finished last night so this morning I manually cloned the `openrxv-items-temp` index to `openrxv-items`
- First check the number of items in the temp index, then set it to read only, then delete the items index, then delete the temp index:
```console
$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
{
"count" : 100046,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items?pretty'
$ curl -s -X POST "http://localhost:9200/openrxv-items-temp/_clone/openrxv-items?pretty"
$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'
{
"count" : 100046,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
```
- Interestingly [the item](https://hdl.handle.net/10568/110447) that we noticed was duplicated now only appears once
- The [missing item](https://hdl.handle.net/10568/110133) is still missing
<!-- 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: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:modified_time" content="2020-12-13T16:16:10+02:00" />
<meta property="article:modified_time" content="2020-12-15T13:13:18+02:00" />
@ -46,9 +46,9 @@ I started processing those (about 411,000 records):
"@type": "BlogPosting",
"headline": "December, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-12/",
"wordCount": "2037",
"wordCount": "2609",
"datePublished": "2020-12-01T11:32:54+02:00",
"dateModified": "2020-12-13T16:16:10+02:00",
"dateModified": "2020-12-15T13:13:18+02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -490,7 +490,122 @@ $ query-json '.items | length' /tmp/policy2.json
<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><h2 id="2020-12-15">2020-12-15</h2>
<ul>
<li>After the re-harvest last night there were 200,000 items in the <code>openrxv-items-temp</code> index again
<ul>
<li>I cleared the core and started a re-harvest, but Peter sent me a bunch of author corrections for CGSpace so I decided to cancel it until after I apply them and re-index Discovery</li>
</ul>
</li>
<li>I checked the 1,534 fixes in Open Refine (had to fix a few UTF-8 errors, as always from Peter&rsquo;s CSVs) and then applied them using the <code>fix-metadata-values.py</code> script:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ ./fix-metadata-values.py -i /tmp/2020-10-28-fix-1534-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3
$ ./delete-metadata-values.py -i /tmp/2020-10-28-delete-2-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -m 3
</code></pre><ul>
<li>Since I was re-indexing Discovery anyways I decided to check for any uppercase AGROVOC and lowercase them:</li>
</ul>
<pre><code class="language-console" data-lang="console">dspace=# BEGIN;
BEGIN
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
UPDATE 406
dspace=# COMMIT;
COMMIT
</code></pre><ul>
<li>I also updated the Font Awesome icon classes for version 5 syntax:</li>
</ul>
<pre><code class="language-console" data-lang="console">dspace=# BEGIN;
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-rss','fas fa-rss', 'g') WHERE text_value LIKE '%fa fa-rss%';
UPDATE 74
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-at','fas fa-at', 'g') WHERE text_value LIKE '%fa fa-at%';
UPDATE 74
dspace=# COMMIT;
</code></pre><ul>
<li>Then I started a full Discovery re-index:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot;
$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
real 265m11.224s
user 171m29.141s
sys 2m41.097s
</code></pre><ul>
<li>Udana sent a report that the WLE approver is experiencing the same issue Peter highlighted a few weeks ago: they are unable to save metadata edits in the workflow</li>
<li>Yesterday Atmire responded about the owningComm and owningColl duplicates in Solr saying they didn&rsquo;t see any anymore&hellip;
<ul>
<li>Indeed I spent a few minutes looking randomly and I didn&rsquo;t find any either&hellip;</li>
<li>I did, however, see lots of duplicates in countryCode_search, countryCode_ngram, ip_search, ip_ngram, userAgent_search, userAgent_ngram, referrer_search, referrer_ngram fields</li>
<li>I sent feedback to them</li>
</ul>
</li>
<li>On the database locking front we haven&rsquo;t had issues in over a week and the Munin graphs look normal:</li>
</ul>
<p><img src="/cgspace-notes/2020/12/postgres_connections_ALL-week2.png" alt="PostgreSQL connections all week">
<img src="/cgspace-notes/2020/12/postgres_locks_ALL-week2.png" alt="PostgreSQL locks all week"></p>
<ul>
<li>After the Discovery re-indexing finished on CGSpace I prepared to start re-harvesting AReS by making sure the <code>openrxv-items-temp</code> index was empty and that the backup index I made yesterday was still there:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
{
&quot;acknowledged&quot; : true
}
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&amp;pretty'
{
&quot;count&quot; : 0,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
$ curl -s 'http://localhost:9200/openrxv-items-2020-12-14/_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><h2 id="2020-12-16">2020-12-16</h2>
<ul>
<li>The harvesting on AReS finished last night so this morning I manually cloned the <code>openrxv-items-temp</code> index to <code>openrxv-items</code>
<ul>
<li>First check the number of items in the temp index, then set it to read only, then delete the items index, then delete 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=*&amp;pretty'
{
&quot;count&quot; : 100046,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
$ 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 -XDELETE 'http://localhost:9200/openrxv-items?pretty'
$ curl -s -X POST &quot;http://localhost:9200/openrxv-items-temp/_clone/openrxv-items?pretty&quot;
$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&amp;pretty'
{
&quot;count&quot; : 100046,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
$ 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}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty'
</code></pre><ul>
<li>Interestingly <a href="https://hdl.handle.net/10568/110447">the item</a> that we noticed was duplicated now only appears once</li>
<li>The <a href="https://hdl.handle.net/10568/110133">missing item</a> is still missing</li>
</ul>
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2020-12-13T16:16:10+02:00" />
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