<li>Validate and register CGSpace on <ahref="https://www.openarchives.org/Register/ValidateSite?log=Z2V7WCT7">OpenArchives</a>
<ul>
<li>Last month IWMI colleagues were asking me to look into this, and after checking the OpenArchives mailing list it seems there was a problem on the server side</li>
<li>Now it has worked and the message is “Successfully updated OAI registration database to status COMPLIANT.”</li>
<li>I received an email (as the Admin contact on our OAI) that says:</li>
</ul>
</li>
</ul>
<blockquote>
<p>Your repository has been registered in the OAI database of conforming repositories.</p>
</blockquote>
<ul>
<li>Now I’m taking a screenshot of the validation page for posterity, because the logs seem to go away after some time</li>
</span><spanstyle="color:#960050;background-color:#1e0010"></span>node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias 'AggregationsAggregate' circularly references itself.
node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias 'AggregationsSingleBucketAggregate' circularly references itself.
<li>Ah, it seems the code on the server was slightly out of date
<ul>
<li>I checked out the latest master branch and it built</li>
</ul>
</li>
</ul>
<h2id="2022-01-12">2022-01-12</h2>
<ul>
<li>Fix some citation formatting issues in Gaia’s <ahref="https://dspacetest.cgiar.org/handle/10568/115230">eighteen CAS Green Cover publications on DSpace Test</a></li>
<li>Francesca was having issues with a submission on CGSpace this week
<ul>
<li>I checked and see a lot of locks in PostgreSQL:</li>
</ul>
</li>
</ul>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><codeclass="language-console"data-lang="console">$ psql -c <spanstyle="color:#e6db74">"SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | sort | uniq -c | sort -n
1
1 ------------------
1 (3506 rows)
1 application_name
9 psql
10
3487 dspaceWeb
</code></pre></div><ul>
<li>As before, I see messages from PostgreSQL about processes waiting for locks since I enabled the <code>log_lock_waits</code> setting last month:</li>
<li>Finalize cleaning up the dates on the CGIAR TAC and IWC records from Gaia</li>
<li>Rebuild AReS and start a fresh harvest</li>
</ul>
<h2id="2022-01-25">2022-01-25</h2>
<ul>
<li>Help Udana from IWMI answer some questions about licenses on their journal articles
<ul>
<li>I was surprised to see they have 921 total, but only about 200 have a <code>dcterms.license</code> field</li>
<li>I updated about thirty manually, but really Udana should do more…</li>
</ul>
</li>
<li>Normalize the metadata <code>text_lang</code> attributes on CGSpace database:</li>
</ul>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><codeclass="language-console"data-lang="console">dspace=# SELECT DISTINCT text_lang, count(text_lang) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) GROUP BY text_lang ORDER BY count DESC;
text_lang | count
-----------+---------
en_US | 2803350
en | 6232
| 3200
fr | 2
vn | 2
92 | 1
sp | 1
| 0
(8 rows)
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('en', '92', '');
UPDATE 9433
</code></pre></div><ul>
<li>Then export the WLE Journal Articles collection again so there are fewer columns to mess with</li>
</ul>
<h2id="2022-01-26">2022-01-26</h2>
<ul>
<li>Send Gaia an example of the duplicate report for the first 200 TAC items to see what she thinks</li>
</ul>
<h2id="2022-01-27">2022-01-27</h2>
<ul>
<li>Work on WLE’s Journal Articles a bit more
<ul>
<li>I realized that ~130 items have DOIs in their citation, but no <code>cg.identifier.doi</code> field</li>
<li>I used this OpenRefine GREL to copy them:</li>
<li>I also spent a bit of time cleaning up ILRI Journal Articles, but I notice that we don’t put DOIs in the citation so it’s not possible to fix items that are missing DOIs that way
<ul>
<li>And I cleaned up and normalized some licenses</li>
</ul>
</li>
<li>Francesca from Bioversity was having issues with a submission on CGSpace again
<ul>
<li>I looked at PostgreSQL and see an increasing number of locks:</li>
</ul>
</li>
</ul>
<divclass="highlight"><pretabindex="0"style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><codeclass="language-console"data-lang="console">$ psql -c <spanstyle="color:#e6db74">"SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | sort | uniq -c | sort -n
<li>I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL
<ul>
<li>The issue in Francesca’s case was actually that someone had taken the task, not that PostgreSQL transactions were locked!</li>
</ul>
</li>
</ul>
<h2id="2022-01-28">2022-01-28</h2>
<ul>
<li>Finalize the last ~100 WLE Journal Article items without licensese and DOIs
<ul>
<li>I did as many as I could, also updating http links to https for many journal links</li>
</ul>
</li>
<li>Federica Bottamedi contacted us from the system office to say that she took over for Vini (Abhilasha Vaid)
<ul>
<li>She created an account on CGSpace and now we need to see which workflows she should belong to</li>
</ul>
</li>
<li>Start a fresh harvesting on AReS</li>
<li>I adjusted the <code>check-duplicates.py</code> script to write the output to a CSV file including the id, both titles, both dates, and the handle link
<ul>
<li>I included the id because I will need a unique field to join the resulting list of non-duplicates with the original CSV where the rest of the metadata and filenames are</li>
<li>Since these items are not in DSpace yet, I generated simple numeric IDs in OpenRefine using this GREL transform: <code>row.index + 1</code></li>
<li>Then I ran <code>check-duplicates.py</code> on items 1–200 and sent the resulting CSV to Gaia</li>
</ul>
</li>
<li>Delete one duplicate item I saw in IITA’s Journal Articles that was uploaded earlier in WLE
<ul>
<li>Also do some general cleanup on IITA’s Journal Articles collection in OpenRefine</li>
</ul>
</li>
<li>Delete one duplicate item I saw in ILRI’s Journal Articles collection
<ul>
<li>Also do some general cleanup on ILRI’s Journal Articles collection in OpenRefine and csv-metadata-quality</li>
</ul>
</li>
</ul>
<h2id="2022-01-29">2022-01-29</h2>
<ul>
<li>I did some more cleanup on the ILRI Journal Articles
<ul>
<li>I added missing journal titles for items that had ISSNs</li>
<li>Then I added pages for items that had them in the citation</li>
<li>First, I faceted the citation field based on whether or not the item had something like “: 232-234” present:</li>
<li>Then I did similar for <code>cg.volume</code> and <code>cg.issue</code>, also based on the citation, for example to extract the “16” from “Journal of Blah 16(1)”, where “16” is the second capture group in a zero-based match:</li>
