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Add notes for 2021-12-19
This commit is contained in:
parent
f5a0ea201e
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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
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- This also includes the mojibake fixes and title/citation checks and some bug fixes
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## 2021-12-09
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- Help Francesca upload the dataset for one CIAT publication (it has like 100 authors so we did it via CSV)
|
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|
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## 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
|
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- Run AReS harvesting
|
||||
|
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## 2021-12-13
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- 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
|
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- 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
|
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- Create a temporary account for Rafael Rodriguez on DSpace Test so he can investigate the submission workflow
|
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- I added him to the admin group on the Alliance community...
|
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## 2021-12-14
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- I finally caught some stuck locks on CGSpace after checking several times per day for the last week:
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```console
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$ psql -c "SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | wc -l
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1508
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```
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||||
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- Now looking at the locks query sorting by age of locks:
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```console
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$ cat locks-age.sql
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SELECT a.datname,
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l.relation::regclass,
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l.transactionid,
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l.mode,
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l.GRANTED,
|
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a.usename,
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a.query,
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a.query_start,
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age(now(), a.query_start) AS "age",
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a.pid
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FROM pg_stat_activity a
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JOIN pg_locks l ON l.pid = a.pid
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ORDER BY a.query_start;
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```
|
||||
|
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- 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
|
||||
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## 2021-12-16
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|
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- 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
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$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=fuuu@fuuu.com --source /tmp/SimpleArchiveFormat --mapfile=./2021-12-16-green-covers.map
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```
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## 2021-12-19
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- I tried to update all Docker containers on AReS and then run a build, but I got an error in the backend:
|
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```console
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> openrxv-backend@0.0.1 build
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> nest build
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node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias 'AggregationsAggregate' circularly references itself.
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2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate<any> | AggregationsTermsAggregate<any> | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate<AggregationsBucket> | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate
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~~~~~~~~~~~~~~~~~~~~~
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node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias 'AggregationsSingleBucketAggregate' circularly references itself.
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3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Found 2 error(s).
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```
|
||||
|
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- 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...
|
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- I made a pull request
|
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- But since software sucks, now I get an error in the frontend while starting nginx:
|
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|
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```console
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nginx: [emerg] host not found in upstream "backend:3000" in /etc/nginx/conf.d/default.conf:2
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```
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||||
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- 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?)
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- 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:
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```console
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$ docker exec -it redis bash
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root@23692d6b51c5:/data# cat /etc/os-release
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PRETTY_NAME="Debian GNU/Linux 11 (bullseye)"
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NAME="Debian GNU/Linux"
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VERSION_ID="11"
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VERSION="11 (bullseye)"
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VERSION_CODENAME=bullseye
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ID=debian
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HOME_URL="https://www.debian.org/"
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SUPPORT_URL="https://www.debian.org/support"
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BUG_REPORT_URL="https://bugs.debian.org/"
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```
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- I bumped the version to 6 on my local test machine and the logs look good:
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```console
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$ docker logs redis
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1:C 19 Dec 2021 19:27:15.583 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
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1:C 19 Dec 2021 19:27:15.583 # Redis version=6.2.6, bits=64, commit=00000000, modified=0, pid=1, just started
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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
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1:M 19 Dec 2021 19:27:15.584 * monotonic clock: POSIX clock_gettime
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1:M 19 Dec 2021 19:27:15.584 * Running mode=standalone, port=6379.
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1:M 19 Dec 2021 19:27:15.584 # Server initialized
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1:M 19 Dec 2021 19:27:15.585 * Loading RDB produced by version 5.0.14
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1:M 19 Dec 2021 19:27:15.585 * RDB age 33 seconds
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1:M 19 Dec 2021 19:27:15.585 * RDB memory usage when created 3.17 Mb
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1:M 19 Dec 2021 19:27:15.595 # Done loading RDB, keys loaded: 932, keys expired: 1.
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1:M 19 Dec 2021 19:27:15.595 * DB loaded from disk: 0.011 seconds
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1:M 19 Dec 2021 19:27:15.595 * Ready to accept connections
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```
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- The interface and harvesting all work as expected...
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- I pushed the update to OpenRXV
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<!-- vim: set sw=2 ts=2: -->
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|
@ -22,7 +22,7 @@ Total number of bot hits purged: 3679
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-12/" />
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<meta property="article:published_time" content="2021-12-01T16:07:07+02:00" />
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<meta property="article:modified_time" content="2021-12-08T08:47:33+02:00" />
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<meta property="article:modified_time" content="2021-12-08T19:34:39+02:00" />
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@ -50,9 +50,9 @@ Total number of bot hits purged: 3679
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"@type": "BlogPosting",
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"headline": "December, 2021",
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"url": "https://alanorth.github.io/cgspace-notes/2021-12/",
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"wordCount": "992",
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"wordCount": "1942",
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"datePublished": "2021-12-01T16:07:07+02:00",
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"dateModified": "2021-12-08T08:47:33+02:00",
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"dateModified": "2021-12-08T19:34:39+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -276,6 +276,158 @@ Purging 34458 hits from HeadlessChrome in statistics
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</ul>
|
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</li>
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</ul>
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<h2 id="2021-12-09">2021-12-09</h2>
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<ul>
|
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<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’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>
|
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<h2 id="2021-12-13">2021-12-13</h2>
|
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<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…</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">"SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | wc -l
|
||||
1508
|
||||
</code></pre></div><ul>
|
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<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
|
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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;
|
||||
</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’t see anything interesting there: only editors making edits…</li>
|
||||
<li>I looked at the nginx REST API logs and saw lots of GET action there from Drupal sites harvesting us…</li>
|
||||
<li>So I’m not sure what it causing this… 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’s <code>log-db-activity.sh</code> script to run every four hours (in the DSpace user’s crontab) so perhaps that will be better than me checking manually</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>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!
|
||||
<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">"-Xmx1024m -Dfile.encoding=UTF-8"</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">> openrxv-backend@0.0.1 build
|
||||
> 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 'AggregationsAggregate' 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<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.
|
||||
<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’m not sure why because I build the backend successfully on my local machine…
|
||||
<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"</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’s that…</li>
|
||||
<li>Pinning <code>~7.15.0</code> allows nest to build fine…</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 "backend:3000" 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’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’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’t expect… 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="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/"
|
||||
</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…
|
||||
<ul>
|
||||
<li>I pushed the update to OpenRXV</li>
|
||||
</ul>
|
||||
</li>
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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|
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||||
|
||||
|
||||
|
@ -3,19 +3,19 @@
|
||||
xmlns:xhtml="http://www.w3.org/1999/xhtml">
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
|
||||
<lastmod>2021-12-08T08:47:33+02:00</lastmod>
|
||||
<lastmod>2021-12-08T19:34:39+02:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2021-12-08T08:47:33+02:00</lastmod>
|
||||
<lastmod>2021-12-08T19:34:39+02:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-12/</loc>
|
||||
<lastmod>2021-12-08T08:47:33+02:00</lastmod>
|
||||
<lastmod>2021-12-08T19:34:39+02:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2021-12-08T08:47:33+02:00</lastmod>
|
||||
<lastmod>2021-12-08T19:34:39+02:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2021-12-08T08:47:33+02:00</lastmod>
|
||||
<lastmod>2021-12-08T19:34:39+02:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-11/</loc>
|
||||
<lastmod>2021-11-30T16:44:30+02:00</lastmod>
|
||||
|
Loading…
Reference in New Issue
Block a user