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Add notes for 2021-12-19

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Alan Orth 2021-12-19 22:03:42 +02:00
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@ -129,4 +129,144 @@ Total number of bot hits purged: 34458
- Finalize country/region changes in csv-metadata-quality checker and release v0.5.0: https://github.com/ilri/csv-metadata-quality/releases/tag/v0.5.0
- This also includes the mojibake fixes and title/citation checks and some bug fixes
## 2021-12-09
- Help Francesca upload the dataset for one CIAT publication (it has like 100 authors so we did it via CSV)
## 2021-12-12
- Patch OpenRXV's Elasticsearch for the CVE-2021-44228 log4j vulnerability and re-deploy AReS
- I added `-Dlog4j2.formatMsgNoLookups=true` to the Elasticsearch Java environment
- Run AReS harvesting
## 2021-12-13
- I ran the `check-duplicates.py` script on the 1,000 items from the CGIAR System Office TAC/ICW/Green Cover archives and found hundreds or thousands of potential duplicates
- I sent feedback to Gaia
- Help Jacquie from WorldFish try to find all outputs for the Fish CRP because there are a few different formats for that name
- Create a temporary account for Rafael Rodriguez on DSpace Test so he can investigate the submission workflow
- I added him to the admin group on the Alliance community...
## 2021-12-14
- I finally caught some stuck locks on CGSpace after checking several times per day for the last week:
```console
$ psql -c "SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | wc -l
1508
```
- Now looking at the locks query sorting by age of locks:
```console
$ cat locks-age.sql
SELECT a.datname,
l.relation::regclass,
l.transactionid,
l.mode,
l.GRANTED,
a.usename,
a.query,
a.query_start,
age(now(), a.query_start) AS "age",
a.pid
FROM pg_stat_activity a
JOIN pg_locks l ON l.pid = a.pid
ORDER BY a.query_start;
```
- The oldest locks are 9 hours and 26 minutes old and the time on the server is `Tue Dec 14 18:41:58 CET 2021`, so it seems something happened around 9:15 this morning
- I looked at the maintenance tasks and there is nothing running around then (only the sitemap update that runs at 8AM, and should be quick)
- I looked at the DSpace log, but didn't see anything interesting there: only editors making edits...
- I looked at the nginx REST API logs and saw lots of GET action there from Drupal sites harvesting us...
- So I'm not sure what it causing this... perhaps something in the XMLUI submission / task workflow
- For now I just ran all system updates and rebooted the server
- I also enabled Atmire's `log-db-activity.sh` script to run every four hours (in the DSpace user's crontab) so perhaps that will be better than me checking manually
- Regarding Gaia's 1,000 items to upload to CGSpace, I checked the eighteen Green Cover records and there are no duplicates, so that's at least a starting point!
- I sent her a spreadsheet with the eighteen items with a new collection column to indicate where they should go
## 2021-12-16
- Working on the CGIAR CAS Green Cover records for Gaia
- Add months to dcterms.issued from PDFs
- Add languages
- Format and fix several authors
- I created a SAF archive with SAFBuilder and then imported it to DSpace Test:
```console
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=fuuu@fuuu.com --source /tmp/SimpleArchiveFormat --mapfile=./2021-12-16-green-covers.map
```
## 2021-12-19
- I tried to update all Docker containers on AReS and then run a build, but I got an error in the backend:
```console
> openrxv-backend@0.0.1 build
> nest build
node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias 'AggregationsAggregate' circularly references itself.
2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate<any> | AggregationsTermsAggregate<any> | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate<AggregationsBucket> | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate
~~~~~~~~~~~~~~~~~~~~~
node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias 'AggregationsSingleBucketAggregate' circularly references itself.
3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Found 2 error(s).
```
- I'm not sure why because I build the backend successfully on my local machine...
- For now I just ran all the system updates and rebooted the machine (linode20)
- Then I started a fresh harvest
- Now I cleared all images on my local machine and I get the same error when building the backend
- It seems to be related to `@elastic/elasticsearch-js`](https://github.com/elastic/elasticsearch-js), which our `package.json` pins with version `^7.13.0"
- I see that AReS is currently using 7.15.0 in its `package-lock.json`, and 7.16.0 was released four days ago so perhaps it's that...
- Pinning `~7.15.0` allows nest to build fine...
- I made a pull request
- But since software sucks, now I get an error in the frontend while starting nginx:
```console
nginx: [emerg] host not found in upstream "backend:3000" in /etc/nginx/conf.d/default.conf:2
```
- In other news, looking at updating our Redis from version 5 to 6 (which is slightly less old, but still old!) and I'm happy to see that the [release notes for version 6](https://raw.githubusercontent.com/redis/redis/6.0/00-RELEASENOTES) say that it is compatible with 5 except for one minor thing that we don't seem to be using (SPOP?)
- For reference I see that our Redis 5 container is based on Debian 11, which I didn't expect... but I still want to try to upgrade to Redis 6 eventually:
```console
$ docker exec -it redis bash
root@23692d6b51c5:/data# cat /etc/os-release
PRETTY_NAME="Debian GNU/Linux 11 (bullseye)"
NAME="Debian GNU/Linux"
VERSION_ID="11"
VERSION="11 (bullseye)"
VERSION_CODENAME=bullseye
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"
```
- I bumped the version to 6 on my local test machine and the logs look good:
```console
$ docker logs redis
1:C 19 Dec 2021 19:27:15.583 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
1:C 19 Dec 2021 19:27:15.583 # Redis version=6.2.6, bits=64, commit=00000000, modified=0, pid=1, just started
1:C 19 Dec 2021 19:27:15.583 # Warning: no config file specified, using the default config. In order to specify a config file use redis-server /path/to/redis.conf
1:M 19 Dec 2021 19:27:15.584 * monotonic clock: POSIX clock_gettime
1:M 19 Dec 2021 19:27:15.584 * Running mode=standalone, port=6379.
1:M 19 Dec 2021 19:27:15.584 # Server initialized
1:M 19 Dec 2021 19:27:15.585 * Loading RDB produced by version 5.0.14
1:M 19 Dec 2021 19:27:15.585 * RDB age 33 seconds
1:M 19 Dec 2021 19:27:15.585 * RDB memory usage when created 3.17 Mb
1:M 19 Dec 2021 19:27:15.595 # Done loading RDB, keys loaded: 932, keys expired: 1.
1:M 19 Dec 2021 19:27:15.595 * DB loaded from disk: 0.011 seconds
1:M 19 Dec 2021 19:27:15.595 * Ready to accept connections
```
- The interface and harvesting all work as expected...
- I pushed the update to OpenRXV
<!-- vim: set sw=2 ts=2: -->

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<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-12/" />
<meta property="article:published_time" content="2021-12-01T16:07:07+02:00" />
<meta property="article:modified_time" content="2021-12-08T08:47:33+02:00" />
<meta property="article:modified_time" content="2021-12-08T19:34:39+02:00" />
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"@type": "BlogPosting",
"headline": "December, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-12/",
"wordCount": "992",
"wordCount": "1942",
"datePublished": "2021-12-01T16:07:07+02:00",
"dateModified": "2021-12-08T08:47:33+02:00",
"dateModified": "2021-12-08T19:34:39+02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -276,6 +276,158 @@ Purging 34458 hits from HeadlessChrome in statistics
</ul>
</li>
</ul>
<h2 id="2021-12-09">2021-12-09</h2>
<ul>
<li>Help Francesca upload the dataset for one CIAT publication (it has like 100 authors so we did it via CSV)</li>
</ul>
<h2 id="2021-12-12">2021-12-12</h2>
<ul>
<li>Patch OpenRXV&rsquo;s Elasticsearch for the CVE-2021-44228 log4j vulnerability and re-deploy AReS
<ul>
<li>I added <code>-Dlog4j2.formatMsgNoLookups=true</code> to the Elasticsearch Java environment</li>
</ul>
</li>
<li>Run AReS harvesting</li>
</ul>
<h2 id="2021-12-13">2021-12-13</h2>
<ul>
<li>I ran the <code>check-duplicates.py</code> script on the 1,000 items from the CGIAR System Office TAC/ICW/Green Cover archives and found hundreds or thousands of potential duplicates
<ul>
<li>I sent feedback to Gaia</li>
</ul>
</li>
<li>Help Jacquie from WorldFish try to find all outputs for the Fish CRP because there are a few different formats for that name</li>
<li>Create a temporary account for Rafael Rodriguez on DSpace Test so he can investigate the submission workflow
<ul>
<li>I added him to the admin group on the Alliance community&hellip;</li>
</ul>
</li>
</ul>
<h2 id="2021-12-14">2021-12-14</h2>
<ul>
<li>I finally caught some stuck locks on CGSpace after checking several times per day for the last week:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ psql -c <span style="color:#e6db74">&#34;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid&#34;</span> | wc -l
1508
</code></pre></div><ul>
<li>Now looking at the locks query sorting by age of locks:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ cat locks-age.sql
SELECT a.datname,
l.relation::regclass,
l.transactionid,
l.mode,
l.GRANTED,
a.usename,
a.query,
a.query_start,
age(now(), a.query_start) AS &#34;age&#34;,
a.pid
FROM pg_stat_activity a
JOIN pg_locks l ON l.pid = a.pid
ORDER BY a.query_start;
</code></pre></div><ul>
<li>The oldest locks are 9 hours and 26 minutes old and the time on the server is <code>Tue Dec 14 18:41:58 CET 2021</code>, so it seems something happened around 9:15 this morning
<ul>
<li>I looked at the maintenance tasks and there is nothing running around then (only the sitemap update that runs at 8AM, and should be quick)</li>
<li>I looked at the DSpace log, but didn&rsquo;t see anything interesting there: only editors making edits&hellip;</li>
<li>I looked at the nginx REST API logs and saw lots of GET action there from Drupal sites harvesting us&hellip;</li>
<li>So I&rsquo;m not sure what it causing this&hellip; perhaps something in the XMLUI submission / task workflow</li>
<li>For now I just ran all system updates and rebooted the server</li>
<li>I also enabled Atmire&rsquo;s <code>log-db-activity.sh</code> script to run every four hours (in the DSpace user&rsquo;s crontab) so perhaps that will be better than me checking manually</li>
</ul>
</li>
<li>Regarding Gaia&rsquo;s 1,000 items to upload to CGSpace, I checked the eighteen Green Cover records and there are no duplicates, so that&rsquo;s at least a starting point!
<ul>
<li>I sent her a spreadsheet with the eighteen items with a new collection column to indicate where they should go</li>
</ul>
</li>
</ul>
<h2 id="2021-12-16">2021-12-16</h2>
<ul>
<li>Working on the CGIAR CAS Green Cover records for Gaia
<ul>
<li>Add months to dcterms.issued from PDFs</li>
<li>Add languages</li>
<li>Format and fix several authors</li>
</ul>
</li>
<li>I created a SAF archive with SAFBuilder and then imported it to DSpace Test:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace import --add --eperson<span style="color:#f92672">=</span>fuuu@fuuu.com --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2021-12-16-green-covers.map
</code></pre></div><h2 id="2021-12-19">2021-12-19</h2>
<ul>
<li>I tried to update all Docker containers on AReS and then run a build, but I got an error in the backend:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">&gt; openrxv-backend@0.0.1 build
&gt; nest build
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias &#39;AggregationsAggregate&#39; circularly references itself.
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate&lt;any&gt; | AggregationsTermsAggregate&lt;any&gt; | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate&lt;AggregationsBucket&gt; | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate
~~~~~~~~~~~~~~~~~~~~~
node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias &#39;AggregationsSingleBucketAggregate&#39; circularly references itself.
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>Found 2 error(s).
</code></pre></div><ul>
<li>I&rsquo;m not sure why because I build the backend successfully on my local machine&hellip;
<ul>
<li>For now I just ran all the system updates and rebooted the machine (linode20)</li>
<li>Then I started a fresh harvest</li>
</ul>
</li>
<li>Now I cleared all images on my local machine and I get the same error when building the backend
<ul>
<li>It seems to be related to <code>@elastic/elasticsearch-js</code>](<a href="https://github.com/elastic/elasticsearch-js)">https://github.com/elastic/elasticsearch-js)</a>, which our <code>package.json</code> pins with version `^7.13.0&quot;</li>
<li>I see that AReS is currently using 7.15.0 in its <code>package-lock.json</code>, and 7.16.0 was released four days ago so perhaps it&rsquo;s that&hellip;</li>
<li>Pinning <code>~7.15.0</code> allows nest to build fine&hellip;</li>
<li>I made a pull request</li>
</ul>
</li>
<li>But since software sucks, now I get an error in the frontend while starting nginx:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">nginx: [emerg] host not found in upstream &#34;backend:3000&#34; in /etc/nginx/conf.d/default.conf:2
</code></pre></div><ul>
<li>In other news, looking at updating our Redis from version 5 to 6 (which is slightly less old, but still old!) and I&rsquo;m happy to see that the <a href="https://raw.githubusercontent.com/redis/redis/6.0/00-RELEASENOTES">release notes for version 6</a> say that it is compatible with 5 except for one minor thing that we don&rsquo;t seem to be using (SPOP?)</li>
<li>For reference I see that our Redis 5 container is based on Debian 11, which I didn&rsquo;t expect&hellip; but I still want to try to upgrade to Redis 6 eventually:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ docker exec -it redis bash
root@23692d6b51c5:/data# cat /etc/os-release
PRETTY_NAME=&#34;Debian GNU/Linux 11 (bullseye)&#34;
NAME=&#34;Debian GNU/Linux&#34;
VERSION_ID=&#34;11&#34;
VERSION=&#34;11 (bullseye)&#34;
VERSION_CODENAME=bullseye
ID=debian
HOME_URL=&#34;https://www.debian.org/&#34;
SUPPORT_URL=&#34;https://www.debian.org/support&#34;
BUG_REPORT_URL=&#34;https://bugs.debian.org/&#34;
</code></pre></div><ul>
<li>I bumped the version to 6 on my local test machine and the logs look good:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-console" data-lang="console">$ docker logs redis
1:C 19 Dec 2021 19:27:15.583 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
1:C 19 Dec 2021 19:27:15.583 # Redis version=6.2.6, bits=64, commit=00000000, modified=0, pid=1, just started
1:C 19 Dec 2021 19:27:15.583 # Warning: no config file specified, using the default config. In order to specify a config file use redis-server /path/to/redis.conf
1:M 19 Dec 2021 19:27:15.584 * monotonic clock: POSIX clock_gettime
1:M 19 Dec 2021 19:27:15.584 * Running mode=standalone, port=6379.
1:M 19 Dec 2021 19:27:15.584 # Server initialized
1:M 19 Dec 2021 19:27:15.585 * Loading RDB produced by version 5.0.14
1:M 19 Dec 2021 19:27:15.585 * RDB age 33 seconds
1:M 19 Dec 2021 19:27:15.585 * RDB memory usage when created 3.17 Mb
1:M 19 Dec 2021 19:27:15.595 # Done loading RDB, keys loaded: 932, keys expired: 1.
1:M 19 Dec 2021 19:27:15.595 * DB loaded from disk: 0.011 seconds
1:M 19 Dec 2021 19:27:15.595 * Ready to accept connections
</code></pre></div><ul>
<li>The interface and harvesting all work as expected&hellip;
<ul>
<li>I pushed the update to OpenRXV</li>
</ul>
</li>
</ul>
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
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