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Add notes for 2021-12
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content/posts/2021-12.md
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content/posts/2021-12.md
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---
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title: "December, 2021"
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date: 2021-12-01T16:07:07+02:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2021-12-01
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- Atmire merged some changes I had submitted to the COUNTER-Robots project
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- I updated our local spider user agents and then re-ran the list with my `check-spider-hits.sh` script on CGSpace:
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```console
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$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
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Purging 1989 hits from The Knowledge AI in statistics
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Purging 1235 hits from MaCoCu in statistics
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Purging 455 hits from WhatsApp in statistics
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Total number of bot hits purged: 3679
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```
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<!--more-->
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## 2021-12-02
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- Francesca from Alliance asked me for help with approving a submission that gets stuck
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- I looked at the PostgreSQL activity and the locks are back up like they were earlier this week
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```console
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$ psql -c "SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | sort | uniq -c | sort -n
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1
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1 ------------------
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1 (1437 rows)
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1 application_name
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9 psql
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1428 dspaceWeb
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```
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- Munin shows the same:
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- Last month I enabled the `log_lock_waits` in PostgreSQL so I checked the log and was surprised to find only a few since I restarted PostgreSQL three days ago:
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```console
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# grep -E '^2021-(11-29|11-30|12-01|12-02)' /var/log/postgresql/postgresql-10-main.log | grep -c 'still waiting for'
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15
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```
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- I think you could analyze the locks for the `dspaceWeb` user (XMLUI) and find out what queries were locking... but it's so much information and I don't know where to start
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- For now I just restarted PostgreSQL...
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- Francesca was able to do her submission immediately...
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- On a related note, I want to enable the `pg_stat_statement` feature to see which queries get run the most, so I created the extension on the CGSpace database
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- I was doing some research on PostgreSQL locks and found some interesting things to consider
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- The default `lock_timeout` is 0, aka disabled
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- The default `statement_timeout` is 0, aka disabled
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- It seems to be recommended to start by setting `statement_timeout` first, rule of thumb [ten times longer than your longest query](https://github.com/jberkus/annotated.conf/blob/master/postgresql.10.simple.conf#L211)
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- Mark Wood mentioned the `checker` cron job that apparently runs in one transaction and might be an issue
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- I definitely saw it holding a bunch of locks for ~30 minutes during the first part of its execution, then it dropped them and did some other less-intensive things without locks
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- Bizuwork was still not receiving emails even after we fixed the SMTP access on CGSpace
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- After some troubleshooting it turns out that the emails from CGSpace were going in her Junk!
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## 2021-12-03
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- I see GARDIAN is now using a "GARDIAN" user agent finally
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- I will add them to our local spider agent override in DSpace so that the hits don't get counted in Solr
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## 2021-12-05
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- Proof fifty records Abenet sent me from Africa Rice Center ("AfricaRice 1st batch Import")
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- Fixed forty-six incorrect collections
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- Cleaned up and normalize affiliations
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- Cleaned up dates (extra `*` character in all?)
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- Cleaned up citation format
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- Fixed some encoding issues in abstracts
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- Removed empty columns
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- Removed one duplicate: Enhancing Rice Productivity and Soil Nitrogen Using Dual-Purpose Cowpea-NERICA® Rice Sequence in Degraded Savanna
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- Added volume and issue metadata by extracting it from the citations
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- All PDFs hosted on davidpublishing.com are dead...
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- All DOIs linking to African Journal of Agricultural Research are dead...
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- Fixed a handful of items marked as "Open Access" that are actually closed
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- Added many missing ISSNs
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- Added many missing countries/regions
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- Fixed invalid AGROVOC terms and added some more based on article subjects
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- I also made some minor changes to the [CSV Metadata Quality Checker](https://github.com/ilri/csv-metadata-quality)
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- Added the ability to check if the item's title exists in the citation
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- Updated to only run the mojibake check if we're not running in unsafe mode (so we don't print the same warning during both the check and fix steps)
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- I ran the re-harvesting on AReS
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<!-- vim: set sw=2 ts=2: -->
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@ -50,7 +50,7 @@ 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": "404",
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"wordCount": "597",
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"datePublished": "2021-12-01T16:07:07+02:00",
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"dateModified": "2021-12-01T16:07:07+02:00",
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"author": {
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@ -191,10 +191,38 @@ Purging 455 hits from WhatsApp in statistics
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<ul>
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<li>I see GARDIAN is now using a “GARDIAN” user agent finally
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<ul>
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<li>I will add them to our local bot override for Solr</li>
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<li>I will add them to our local spider agent override in DSpace so that the hits don’t get counted in Solr</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-12-05">2021-12-05</h2>
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<ul>
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<li>Proof fifty records Abenet sent me from Africa Rice Center (“AfricaRice 1st batch Import”)
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<ul>
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<li>Fixed forty-six incorrect collections</li>
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<li>Cleaned up and normalize affiliations</li>
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<li>Cleaned up dates (extra <code>*</code> character in all?)</li>
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<li>Cleaned up citation format</li>
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<li>Fixed some encoding issues in abstracts</li>
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<li>Removed empty columns</li>
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<li>Removed one duplicate: Enhancing Rice Productivity and Soil Nitrogen Using Dual-Purpose Cowpea-NERICA® Rice Sequence in Degraded Savanna</li>
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<li>Added volume and issue metadata by extracting it from the citations</li>
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<li>All PDFs hosted on davidpublishing.com are dead…</li>
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<li>All DOIs linking to African Journal of Agricultural Research are dead…</li>
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<li>Fixed a handful of items marked as “Open Access” that are actually closed</li>
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<li>Added many missing ISSNs</li>
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<li>Added many missing countries/regions</li>
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<li>Fixed invalid AGROVOC terms and added some more based on article subjects</li>
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</ul>
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</li>
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<li>I also made some minor changes to the <a href="https://github.com/ilri/csv-metadata-quality">CSV Metadata Quality Checker</a>
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<ul>
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<li>Added the ability to check if the item’s title exists in the citation</li>
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<li>Updated to only run the mojibake check if we’re not running in unsafe mode (so we don’t print the same warning during both the check and fix steps)</li>
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</ul>
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</li>
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<li>I ran the re-harvesting on AReS</li>
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</ul>
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<!-- raw HTML omitted -->
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