Add notes
This commit is contained in:
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0FB860CC9C45B1B9
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@ -249,6 +249,102 @@ Total number of hits from bots: 295492
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$ ./ilri/fix-metadata-values.py -i /tmp/authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3
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```
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- Then I imported to CGSpace and started a full Discovery re-index
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- Then I imported to CGSpace and started a full Discovery re-index:
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```console
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$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 272m43.818s
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user 183m4.543s
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sys 2m47.988
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```
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## 2021-11-28
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- Run system updates on AReS server (linode20) and update all Docker containers and reboot
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- Then I started a fresh harvest as I always do on Sunday
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- I am experimenting with pinning npm version 7 on OpenRXV frontend because of these Angular errors:
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```console
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npm WARN EBADENGINE Unsupported engine {
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npm WARN EBADENGINE package: '@angular-devkit/architect@0.901.15',
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npm WARN EBADENGINE required: { node: '>= 10.13.0', npm: '^6.11.0 || ^7.5.6', yarn: '>= 1.13.0' },
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npm WARN EBADENGINE current: { node: 'v12.22.7', npm: '8.1.3' }
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npm WARN EBADENGINE }
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```
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## 2021-11-29
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- Tezira reached out to me to say that submissions on CGSpace are taking forever
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- I see a definite increase in locks in the last few days:
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- The locks are all held by dspaceWeb (XMLUI):
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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 (1394 rows)
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1 application_name
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9 psql
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1385 dspaceWeb
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```
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- I restarted PostgreSQL and the locks dropped down:
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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 (103 rows)
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1 application_name
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9 psql
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94 dspaceWeb
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```
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## 2021-11-30
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- IWMI sent me ORCID identifiers for some new staff
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- We currently have 1332 unique identifiers, so this adds sixteen new ones:
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```console
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$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/iwmi-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2021-11-30-combined-orcids.txt
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$ wc -l /tmp/2021-11-30-combined-orcids.txt
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1348 /tmp/2021-11-30-combined-orcids.txt
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```
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- After I combined them and removed duplicates, I resolved all the names using my `resolve-orcids.py` script:
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```console
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$ ./ilri/resolve-orcids.py -i /tmp/2021-11-30-combined-orcids.txt -o /tmp/2021-11-30-combined-orcids-names.txt
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```
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- Then I updated some ORCID identifiers that had changed in the XML:
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```console
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$ cat 2021-11-30-fix-orcids.csv
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cg.creator.identifier,correct
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"ADEBOWALE AKANDE: 0000-0002-6521-3272","ADEBOWALE AD AKANDE: 0000-0002-6521-3272"
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"Daniel Ortiz Gonzalo: 0000-0002-5517-1785","Daniel Ortiz-Gonzalo: 0000-0002-5517-1785"
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"FRIDAY ANETOR: 0000-0003-3137-1958","Friday Osemenshan Anetor: 0000-0003-3137-1958"
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"Sander Muilerman: 0000-0001-9103-3294","Sander Muilerman-Rodrigo: 0000-0001-9103-3294"
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$ ./ilri/fix-metadata-values.py -i 2021-11-30-fix-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.identifier -t 'correct' -m 247
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```
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- Tag existing items from the IWMI's new authors with ORCID iDs using `add-orcid-identifiers-csv.py` (7 new metadata fields added):
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```console
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$ cat 2021-11-30-add-orcids.csv
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dc.contributor.author,cg.creator.identifier
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"Liaqat, U.W.","Umar Waqas Liaqat: 0000-0001-9027-5232"
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"Liaqat, Umar Waqas","Umar Waqas Liaqat: 0000-0001-9027-5232"
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"Munyaradzi, M.","Munyaradzi Junia Mutenje: 0000-0002-7829-9300"
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"Mutenje, Munyaradzi","Munyaradzi Junia Mutenje: 0000-0002-7829-9300"
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"Rex, William","William Rex: 0000-0003-4979-5257"
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"Shrestha, Shisher","Nirman Shrestha: 0000-0002-0996-8611"
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$ ./ilri/add-orcid-identifiers-csv.py -i 2021-11-30-add-orcids.csv -db dspace -u dspace -p 'fuuu'
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```
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<!-- vim: set sw=2 ts=2: -->
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@ -18,7 +18,7 @@ $ zstd statistics-2019.json
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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/2021-11/" />
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<meta property="article:published_time" content="2021-11-02T22:27:07+02:00" />
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<meta property="article:modified_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="article:modified_time" content="2021-11-27T14:37:33+02:00" />
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@ -42,9 +42,9 @@ $ zstd statistics-2019.json
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"@type": "BlogPosting",
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"headline": "November, 2021",
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"url": "https://alanorth.github.io/cgspace-notes/2021-11/",
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"wordCount": "1682",
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"wordCount": "2080",
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"datePublished": "2021-11-02T22:27:07+02:00",
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"dateModified": "2021-11-27T12:18:52+02:00",
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"dateModified": "2021-11-27T14:37:33+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -389,9 +389,91 @@ Found 3 hits from 188.134.31.88 in statistics
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</ul>
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<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">$ ./ilri/fix-metadata-values.py -i /tmp/authors.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -f dc.contributor.author -t <span style="color:#e6db74">'correct'</span> -m <span style="color:#ae81ff">3</span>
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</code></pre></div><ul>
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<li>Then I imported to CGSpace and started a full Discovery re-index</li>
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<li>Then I imported to CGSpace and started a full Discovery re-index:</li>
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</ul>
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<!-- raw HTML omitted -->
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<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">$ time chrt -b <span style="color:#ae81ff">0</span> ionice -c2 -n7 nice -n19 dspace index-discovery -b
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<span style="color:#960050;background-color:#1e0010">
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</span><span style="color:#960050;background-color:#1e0010"></span>real 272m43.818s
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user 183m4.543s
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sys 2m47.988
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</code></pre></div><h2 id="2021-11-28">2021-11-28</h2>
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<ul>
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<li>Run system updates on AReS server (linode20) and update all Docker containers and reboot
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<ul>
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<li>Then I started a fresh harvest as I always do on Sunday</li>
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</ul>
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</li>
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<li>I am experimenting with pinning npm version 7 on OpenRXV frontend because of these Angular errors:</li>
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</ul>
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<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">npm WARN EBADENGINE Unsupported engine {
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npm WARN EBADENGINE package: '@angular-devkit/architect@0.901.15',
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npm WARN EBADENGINE required: { node: '>= 10.13.0', npm: '^6.11.0 || ^7.5.6', yarn: '>= 1.13.0' },
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npm WARN EBADENGINE current: { node: 'v12.22.7', npm: '8.1.3' }
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npm WARN EBADENGINE }
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</code></pre></div><h2 id="2021-11-29">2021-11-29</h2>
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<ul>
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<li>Tezira reached out to me to say that submissions on CGSpace are taking forever</li>
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<li>I see a definite increase in locks in the last few days:</li>
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</ul>
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<p><img src="/cgspace-notes/2021/11/postgres_locks_ALL-week.png" alt="PostgreSQL locks week"></p>
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<ul>
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<li>The locks are all held by dspaceWeb (XMLUI):</li>
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</ul>
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<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 application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | sort | uniq -c | sort -n
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1
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1 ------------------
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1 (1394 rows)
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1 application_name
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9 psql
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1385 dspaceWeb
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</code></pre></div><ul>
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<li>I restarted PostgreSQL and the locks dropped down:</li>
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</ul>
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<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 application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | sort | uniq -c | sort -n
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1
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1 ------------------
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1 (103 rows)
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1 application_name
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9 psql
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94 dspaceWeb
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</code></pre></div><h2 id="2021-11-30">2021-11-30</h2>
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<ul>
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<li>IWMI sent me ORCID identifiers for some new staff
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<ul>
|
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<li>We currently have 1332 unique identifiers, so this adds sixteen new ones:</li>
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</ul>
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</li>
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</ul>
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<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 ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/iwmi-orcids.txt | grep -oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort | uniq > /tmp/2021-11-30-combined-orcids.txt
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$ wc -l /tmp/2021-11-30-combined-orcids.txt
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1348 /tmp/2021-11-30-combined-orcids.txt
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</code></pre></div><ul>
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<li>After I combined them and removed duplicates, I resolved all the names using my <code>resolve-orcids.py</code> script:</li>
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</ul>
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<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">$ ./ilri/resolve-orcids.py -i /tmp/2021-11-30-combined-orcids.txt -o /tmp/2021-11-30-combined-orcids-names.txt
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</code></pre></div><ul>
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<li>Then I updated some ORCID identifiers that had changed in the XML:</li>
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</ul>
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<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 2021-11-30-fix-orcids.csv
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cg.creator.identifier,correct
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"ADEBOWALE AKANDE: 0000-0002-6521-3272","ADEBOWALE AD AKANDE: 0000-0002-6521-3272"
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"Daniel Ortiz Gonzalo: 0000-0002-5517-1785","Daniel Ortiz-Gonzalo: 0000-0002-5517-1785"
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"FRIDAY ANETOR: 0000-0003-3137-1958","Friday Osemenshan Anetor: 0000-0003-3137-1958"
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"Sander Muilerman: 0000-0001-9103-3294","Sander Muilerman-Rodrigo: 0000-0001-9103-3294"
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$ ./ilri/fix-metadata-values.py -i 2021-11-30-fix-orcids.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -f cg.creator.identifier -t <span style="color:#e6db74">'correct'</span> -m <span style="color:#ae81ff">247</span>
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</code></pre></div><ul>
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<li>Tag existing items from the IWMI’s new authors with ORCID iDs using <code>add-orcid-identifiers-csv.py</code> (7 new metadata fields added):</li>
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</ul>
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<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 2021-11-30-add-orcids.csv
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dc.contributor.author,cg.creator.identifier
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"Liaqat, U.W.","Umar Waqas Liaqat: 0000-0001-9027-5232"
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"Liaqat, Umar Waqas","Umar Waqas Liaqat: 0000-0001-9027-5232"
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"Munyaradzi, M.","Munyaradzi Junia Mutenje: 0000-0002-7829-9300"
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"Mutenje, Munyaradzi","Munyaradzi Junia Mutenje: 0000-0002-7829-9300"
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"Rex, William","William Rex: 0000-0003-4979-5257"
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"Shrestha, Shisher","Nirman Shrestha: 0000-0002-0996-8611"
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$ ./ilri/add-orcid-identifiers-csv.py -i 2021-11-30-add-orcids.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span>
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</code></pre></div><!-- raw HTML omitted -->
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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||||
<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
|
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+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/" />
|
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+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/posts/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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<meta property="og:updated_time" content="2021-11-27T14:37:33+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" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
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||||
<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
|
||||
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||||
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@ -10,7 +10,7 @@
|
|||
<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/posts/" />
|
||||
<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
|
||||
<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
|
||||
<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
|
||||
<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
|
||||
<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-11-27T12:18:52+02:00" />
|
||||
<meta property="og:updated_time" content="2021-11-27T14:37:33+02:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -3,19 +3,19 @@
|
|||
xmlns:xhtml="http://www.w3.org/1999/xhtml">
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
|
||||
<lastmod>2021-11-27T12:18:52+02:00</lastmod>
|
||||
<lastmod>2021-11-27T14:37:33+02:00</lastmod>
|
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</url><url>
|
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2021-11-27T12:18:52+02:00</lastmod>
|
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<lastmod>2021-11-27T14:37:33+02:00</lastmod>
|
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</url><url>
|
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<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2021-11-27T12:18:52+02:00</lastmod>
|
||||
<lastmod>2021-11-27T14:37:33+02:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-11/</loc>
|
||||
<lastmod>2021-11-27T12:18:52+02:00</lastmod>
|
||||
<lastmod>2021-11-27T14:37:33+02:00</lastmod>
|
||||
</url><url>
|
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<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2021-11-27T12:18:52+02:00</lastmod>
|
||||
<lastmod>2021-11-27T14:37:33+02:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-10/</loc>
|
||||
<lastmod>2021-11-01T10:48:13+02:00</lastmod>
|
||||
|
|
|
|||
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Reference in New Issue