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Alan Orth 2022-01-27 16:58:05 +03:00
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88
content/posts/2022-01.md
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@ -88,4 +88,92 @@ $ grep -E '^2022-01*' /var/log/postgresql/postgresql-10-main.log | grep -c 'stil
- I set a system alert on DSpace and then restarted the server
## 2022-01-20
- Abenet gave me a thumbs up for Gaia's eighteen CAS Green Cover items from last month
- I created a SimpleArchiveFormat bundle with SAFBuilder and then imported them on CGSpace:
```console
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile=./2022-01-20-green-covers.map
```
## 2022-01-21
- Start working on the rest of the ~980 CGIAR TAC and ICW documents from Gaia
- I did some cleanups and standardization of author names
- I also noticed that a few dozen items had no dates at all, so I checked the PDFs and found dates for them in the text
- Otherwise all items have only a year, which is not great...
- Proof of concept upgrade of OpenRXV from Angular 9 to Angular 10
- I did some basic tests and created a [pull request](https://github.com/ilri/OpenRXV/pull/128)
## 2022-01-22
- Spend some time adding months to the CGIAR TAC and IWC records from Gaia
- Most of the PDFs have months so this is annoying...
## 2022-01-23
- Finalize cleaning up the dates on the CGIAR TAC and IWC records from Gaia
- Rebuild AReS and start a fresh harvest
## 2022-01-25
- Help Udana from IWMI answer some questions about licenses on their journal articles
- I was surprised to see they have 921 total, but only about 200 have a `dcterms.license` field
- I updated about thirty manually, but really Udana should do more...
- Normalize the metadata `text_lang` attributes on CGSpace database:
```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
```
- Then export the WLE Journal Articles collection again so there are fewer columns to mess with
## 2022-01-26
- Send Gaia an example of the duplicate report for the first 200 TAC items to see what she thinks
## 2022-01-27
- Work on WLE's Journal Articles a bit more
- I realized that ~130 items have DOIs in their citation, but no `cg.identifier.doi` field
- I used this OpenRefine GREL to copy them:
```
cells['dcterms.bibliographicCitation[en_US]'].value.split("doi: ")[1]
```
- 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
- And I cleaned up and normalized some licenses
- Francesca from Bioversity was having issues with a submission on CGSpace again
- I looked at PostgreSQL and see an increasing number of locks:
```console
$ 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
1
1 ------------------
1 (537 rows)
1 application_name
9 psql
51 dspaceApi
477 dspaceWeb
$ grep -E '^2022-01*' /var/log/postgresql/postgresql-10-main.log | grep -c 'still waiting for'
3
```
- I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL
<!-- vim: set sw=2 ts=2: -->

109
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@ -14,7 +14,7 @@ Start a full harvest on AReS
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-01/" />
<meta property="article:published_time" content="2022-01-01T15:20:54+02:00" />
<meta property="article:modified_time" content="2022-01-12T19:55:47+02:00" />
<meta property="article:modified_time" content="2022-01-19T18:14:26+03:00" />
@ -34,9 +34,9 @@ Start a full harvest on AReS
"@type": "BlogPosting",
"headline": "January, 2022",
"url": "https://alanorth.github.io/cgspace-notes/2022-01/",
"wordCount": "366",
"wordCount": "855",
"datePublished": "2022-01-01T15:20:54+02:00",
"dateModified": "2022-01-12T19:55:47+02:00",
"dateModified": "2022-01-19T18:14:26+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -196,6 +196,109 @@ node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type
</code></pre></div><ul>
<li>I set a system alert on DSpace and then restarted the server</li>
</ul>
<h2 id="2022-01-20">2022-01-20</h2>
<ul>
<li>Abenet gave me a thumbs up for Gaia&rsquo;s eighteen CAS Green Cover items from last month
<ul>
<li>I created a SimpleArchiveFormat bundle with SAFBuilder and then imported them on CGSpace:</li>
</ul>
</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>aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-01-20-green-covers.map
</code></pre></div><h2 id="2022-01-21">2022-01-21</h2>
<ul>
<li>Start working on the rest of the ~980 CGIAR TAC and ICW documents from Gaia
<ul>
<li>I did some cleanups and standardization of author names</li>
<li>I also noticed that a few dozen items had no dates at all, so I checked the PDFs and found dates for them in the text</li>
<li>Otherwise all items have only a year, which is not great&hellip;</li>
</ul>
</li>
<li>Proof of concept upgrade of OpenRXV from Angular 9 to Angular 10
<ul>
<li>I did some basic tests and created a <a href="https://github.com/ilri/OpenRXV/pull/128">pull request</a></li>
</ul>
</li>
</ul>
<h2 id="2022-01-22">2022-01-22</h2>
<ul>
<li>Spend some time adding months to the CGIAR TAC and IWC records from Gaia
<ul>
<li>Most of the PDFs have months so this is annoying&hellip;</li>
</ul>
</li>
</ul>
<h2 id="2022-01-23">2022-01-23</h2>
<ul>
<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>
<h2 id="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&hellip;</li>
</ul>
</li>
<li>Normalize the metadata <code>text_lang</code> attributes on CGSpace database:</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">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=&#39;en_US&#39; WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN (&#39;en&#39;, &#39;92&#39;, &#39;&#39;);
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>
<h2 id="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>
<h2 id="2022-01-27">2022-01-27</h2>
<ul>
<li>Work on WLE&rsquo;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>
</ul>
</li>
</ul>
<pre tabindex="0"><code>cells['dcterms.bibliographicCitation[en_US]'].value.split(&quot;doi: &quot;)[1]
</code></pre><ul>
<li>I also spent a bit of time cleaning up ILRI Journal Articles, but I notice that we don&rsquo;t put DOIs in the citation so it&rsquo;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>
<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 application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid&#34;</span> | sort | uniq -c | sort -n
1
1 ------------------
1 (537 rows)
1 application_name
9 psql
51 dspaceApi
477 dspaceWeb
$ grep -E <span style="color:#e6db74">&#39;^2022-01*&#39;</span> /var/log/postgresql/postgresql-10-main.log | grep -c <span style="color:#e6db74">&#39;still waiting for&#39;</span>
3
</code></pre></div><ul>
<li>I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL</li>
</ul>
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2022-01-12T19:55:47+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-01-12T19:55:47+02:00" />
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-01-12T19:55:47+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-01-12T19:55:47+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-01-12T19:55:47+02:00" />
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</url><url>
<loc>https://alanorth.github.io/cgspace-notes/2021-12/</loc>
<lastmod>2022-01-09T10:39:51+02:00</lastmod>