Add notes for 2021-10-06
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@ -120,4 +120,52 @@ $ ./ilri/check-spider-ip-hits.sh -f /tmp/robot-ips.txt -p
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Total number of bot hits purged: 465119
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```
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## 2021-10-06
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- Thinking about how we could check for duplicates before importing
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- I found out that [PostgreSQL has a built-in similarity function](https://www.freecodecamp.org/news/fuzzy-string-matching-with-postgresql/):
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```console
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localhost/dspace63= > CREATE EXTENSION pg_trgm;
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localhost/dspace63= > SELECT metadata_value_id, text_value, dspace_object_id FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND SIMILARITY(text_value,'Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines') > 0.5;
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metadata_value_id │ text_value │ dspace_object_id
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───────────────────┼────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
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3652624 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ b7f0bf12-b183-4b2f-bbd2-7a5697b0c467
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3677663 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ fb62f551-f4a5-4407-8cdc-6bff6dac399e
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(2 rows)
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```
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- I was able to find an exact duplicate for an IITA item by searching for its title (I already knew that these existed)
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- I started working on a basic Python script to do this and managed to find an actual duplicate in the recent IWMI items
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- I think I will check for similar titles, and if I find them I will print out the handles for verification
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- I could also proceed to check other metadata like type because those shouldn't vary too much
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- I ran my new `check-duplicates.py` script on the 292 non-IWMI publications from Udana and found twelve potential duplicates
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- Upon checking them manually, I found that 7/12 were indeed already present on CGSpace!
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- This is with the similarity threshold at 0.5. I wonder if tweaking that higher will make the script run faster and eliminate some false positives
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- I re-ran it with higher thresholds this eliminated all false positives, but it still took 24 minutes to run for 292 items!
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- 0.6: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.09s user 0.03s system 0% cpu 24:40.42 total
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- 0.7: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.12s user 0.03s system 0% cpu 24:29.15 total
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- 0.8: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.09s user 0.03s system 0% cpu 25:44.13 total
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- Some minor updates to csv-metadata-quality
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- Fix two issues with regular expressions in the duplicate items and experimental language checks
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- Add a check for items that have a DOI listed in their citation, but are missing a standalone DOI field
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- Then I ran this new version of csv-metadata-quality on an export of IWMI's community, minus some fields I don't want to check:
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```console
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$ csvcut -C 'dc.date.accessioned,dc.date.accessioned[],dc.date.accessioned[en_US],dc.date.available,dc.date.available[],dc.date.available[en_US],dcterms.issued[en_US],dcterms.issued[],dcterms.issued,dc.description.provenance[en],dc.description.provenance[en_US],dc.identifier.uri,dc.identifier.uri[],dc.identifier.uri[en_US],dcterms.abstract[en_US],dcterms.bibliographicCitation[en_US],collection' ~/Downloads/iwmi.csv > /tmp/iwmi-to-check.csv
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$ csv-metadata-quality -i /tmp/iwmi-to-check.csv -o /tmp/iwmi.csv | tee /tmp/out.log
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$ xsv split -s 2000 /tmp /tmp/iwmi.csv
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```
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- I noticed each CSV only had 10 or 20 corrections, mostly that none of the duplicate metadata values were removed in the CSVs...
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- I cut a subset of the fields from the main CSV and tried again, but DSpace said "no changes detected"
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- The duplicates are definitely removed from the CSV, but DSpace doesn't detect them
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- I realized this is an issue I've had before, but forgot because I usually use csv-metadata-quality for new items, not ones already inside DSpace!
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- I found a comment on thread on the dspace-tech mailing list from helix84 in 2015 ("No changes were detected" when importing metadata via XMLUI") where he says:
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> It's very likely that multiple values in a single field are being compared as an unordered set rather than an ordered list.
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> Try doing it in two imports. In first import, remove all authors. In second import, add them in the new order.
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- Shit, so that's worth looking into...
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<!-- vim: set sw=2 ts=2: -->
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@ -25,7 +25,7 @@ So we have 1879/7100 (26.46%) matching already
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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/2021-10/" />
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<meta property="article:published_time" content="2021-10-01T11:14:07+03:00" />
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<meta property="article:modified_time" content="2021-10-04T19:40:13+03:00" />
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<meta property="article:modified_time" content="2021-10-05T18:54:39+03:00" />
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@ -56,9 +56,9 @@ So we have 1879/7100 (26.46%) matching already
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"@type": "BlogPosting",
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"headline": "October, 2021",
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"url": "https://alanorth.github.io/cgspace-notes/2021-10/",
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"wordCount": "771",
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"wordCount": "1307",
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"datePublished": "2021-10-01T11:14:07+03:00",
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"dateModified": "2021-10-04T19:40:13+03:00",
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"dateModified": "2021-10-05T18:54:39+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -247,7 +247,71 @@ $ csvgrep -c 'number of matches' -m '0' /tmp/agrovoc-matches.csv | csvcut -c 1 &
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...
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Total number of bot hits purged: 465119
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</code></pre><!-- raw HTML omitted -->
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</code></pre><h2 id="2021-10-06">2021-10-06</h2>
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<ul>
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<li>Thinking about how we could check for duplicates before importing
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<ul>
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<li>I found out that <a href="https://www.freecodecamp.org/news/fuzzy-string-matching-with-postgresql/">PostgreSQL has a built-in similarity function</a>:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= > CREATE EXTENSION pg_trgm;
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localhost/dspace63= > SELECT metadata_value_id, text_value, dspace_object_id FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND SIMILARITY(text_value,'Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines') > 0.5;
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metadata_value_id │ text_value │ dspace_object_id
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───────────────────┼────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
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3652624 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ b7f0bf12-b183-4b2f-bbd2-7a5697b0c467
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3677663 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ fb62f551-f4a5-4407-8cdc-6bff6dac399e
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(2 rows)
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</code></pre><ul>
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<li>I was able to find an exact duplicate for an IITA item by searching for its title (I already knew that these existed)</li>
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<li>I started working on a basic Python script to do this and managed to find an actual duplicate in the recent IWMI items
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<ul>
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<li>I think I will check for similar titles, and if I find them I will print out the handles for verification</li>
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<li>I could also proceed to check other metadata like type because those shouldn’t vary too much</li>
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</ul>
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</li>
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<li>I ran my new <code>check-duplicates.py</code> script on the 292 non-IWMI publications from Udana and found twelve potential duplicates
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<ul>
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<li>Upon checking them manually, I found that 7/12 were indeed already present on CGSpace!</li>
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<li>This is with the similarity threshold at 0.5. I wonder if tweaking that higher will make the script run faster and eliminate some false positives</li>
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<li>I re-ran it with higher thresholds this eliminated all false positives, but it still took 24 minutes to run for 292 items!
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<ul>
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<li>0.6: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.09s user 0.03s system 0% cpu 24:40.42 total</li>
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<li>0.7: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.12s user 0.03s system 0% cpu 24:29.15 total</li>
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<li>0.8: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.09s user 0.03s system 0% cpu 25:44.13 total</li>
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</ul>
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</li>
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</ul>
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</li>
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<li>Some minor updates to csv-metadata-quality
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<ul>
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<li>Fix two issues with regular expressions in the duplicate items and experimental language checks</li>
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<li>Add a check for items that have a DOI listed in their citation, but are missing a standalone DOI field</li>
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</ul>
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</li>
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<li>Then I ran this new version of csv-metadata-quality on an export of IWMI’s community, minus some fields I don’t want to check:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -C 'dc.date.accessioned,dc.date.accessioned[],dc.date.accessioned[en_US],dc.date.available,dc.date.available[],dc.date.available[en_US],dcterms.issued[en_US],dcterms.issued[],dcterms.issued,dc.description.provenance[en],dc.description.provenance[en_US],dc.identifier.uri,dc.identifier.uri[],dc.identifier.uri[en_US],dcterms.abstract[en_US],dcterms.bibliographicCitation[en_US],collection' ~/Downloads/iwmi.csv > /tmp/iwmi-to-check.csv
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$ csv-metadata-quality -i /tmp/iwmi-to-check.csv -o /tmp/iwmi.csv | tee /tmp/out.log
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$ xsv split -s 2000 /tmp /tmp/iwmi.csv
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</code></pre><ul>
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<li>I noticed each CSV only had 10 or 20 corrections, mostly that none of the duplicate metadata values were removed in the CSVs…
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<ul>
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<li>I cut a subset of the fields from the main CSV and tried again, but DSpace said “no changes detected”</li>
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<li>The duplicates are definitely removed from the CSV, but DSpace doesn’t detect them</li>
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<li>I realized this is an issue I’ve had before, but forgot because I usually use csv-metadata-quality for new items, not ones already inside DSpace!</li>
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<li>I found a comment on thread on the dspace-tech mailing list from helix84 in 2015 (“No changes were detected” when importing metadata via XMLUI") where he says:</li>
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</ul>
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</li>
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</ul>
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<blockquote>
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<p>It’s very likely that multiple values in a single field are being compared as an unordered set rather than an ordered list.
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Try doing it in two imports. In first import, remove all authors. In second import, add them in the new order.</p>
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</blockquote>
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<ul>
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<li>Shit, so that’s worth looking into…</li>
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</ul>
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<!-- 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="2021-10-04T19:40:13+03:00" />
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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:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-10-04T19:40:13+03:00" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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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="2021-10-04T19:40:13+03:00" />
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<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
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@ -10,7 +10,7 @@
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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="2021-10-04T19:40:13+03:00" />
|
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<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
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@ -10,7 +10,7 @@
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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="2021-10-04T19:40:13+03:00" />
|
||||
<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
|
||||
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||||
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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="2021-10-04T19:40:13+03:00" />
|
||||
<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -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" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-10-04T19:40:13+03:00" />
|
||||
<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -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" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-10-04T19:40:13+03:00" />
|
||||
<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -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" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-10-04T19:40:13+03:00" />
|
||||
<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -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" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2021-10-04T19:40:13+03:00" />
|
||||
<meta property="og:updated_time" content="2021-10-05T18:54:39+03:00" />
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -3,19 +3,19 @@
|
|||
xmlns:xhtml="http://www.w3.org/1999/xhtml">
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
|
||||
<lastmod>2021-10-04T19:40:13+03:00</lastmod>
|
||||
<lastmod>2021-10-05T18:54:39+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2021-10-04T19:40:13+03:00</lastmod>
|
||||
<lastmod>2021-10-05T18:54:39+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2021-10-04T19:40:13+03:00</lastmod>
|
||||
<lastmod>2021-10-05T18:54:39+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-10/</loc>
|
||||
<lastmod>2021-10-04T19:40:13+03:00</lastmod>
|
||||
<lastmod>2021-10-05T18:54:39+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2021-10-04T19:40:13+03:00</lastmod>
|
||||
<lastmod>2021-10-05T18:54:39+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-09/</loc>
|
||||
<lastmod>2021-10-04T11:10:54+03:00</lastmod>
|
||||
|
|
|
|||
Loading…
Reference in New Issue