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Add notes for 2021-10-06

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Alan Orth 2021-10-07 08:27:39 +03:00
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content/posts/2021-10.md
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@ -120,4 +120,52 @@ $ ./ilri/check-spider-ip-hits.sh -f /tmp/robot-ips.txt -p
Total number of bot hits purged: 465119
```
## 2021-10-06
- Thinking about how we could check for duplicates before importing
- I found out that [PostgreSQL has a built-in similarity function](https://www.freecodecamp.org/news/fuzzy-string-matching-with-postgresql/):
```console
localhost/dspace63= > CREATE EXTENSION pg_trgm;
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;
metadata_value_id │ text_value │ dspace_object_id
───────────────────┼────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
3652624 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ b7f0bf12-b183-4b2f-bbd2-7a5697b0c467
3677663 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ fb62f551-f4a5-4407-8cdc-6bff6dac399e
(2 rows)
```
- I was able to find an exact duplicate for an IITA item by searching for its title (I already knew that these existed)
- I started working on a basic Python script to do this and managed to find an actual duplicate in the recent IWMI items
- I think I will check for similar titles, and if I find them I will print out the handles for verification
- I could also proceed to check other metadata like type because those shouldn't vary too much
- I ran my new `check-duplicates.py` script on the 292 non-IWMI publications from Udana and found twelve potential duplicates
- Upon checking them manually, I found that 7/12 were indeed already present on CGSpace!
- 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
- I re-ran it with higher thresholds this eliminated all false positives, but it still took 24 minutes to run for 292 items!
- 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
- 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
- 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
- Some minor updates to csv-metadata-quality
- Fix two issues with regular expressions in the duplicate items and experimental language checks
- Add a check for items that have a DOI listed in their citation, but are missing a standalone DOI field
- 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:
```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
$ csv-metadata-quality -i /tmp/iwmi-to-check.csv -o /tmp/iwmi.csv | tee /tmp/out.log
$ xsv split -s 2000 /tmp /tmp/iwmi.csv
```
- I noticed each CSV only had 10 or 20 corrections, mostly that none of the duplicate metadata values were removed in the CSVs...
- I cut a subset of the fields from the main CSV and tried again, but DSpace said "no changes detected"
- The duplicates are definitely removed from the CSV, but DSpace doesn't detect them
- 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!
- 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:
> It's very likely that multiple values in a single field are being compared as an unordered set rather than an ordered list.
> Try doing it in two imports. In first import, remove all authors. In second import, add them in the new order.
- Shit, so that's worth looking into...
<!-- vim: set sw=2 ts=2: -->

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@ -25,7 +25,7 @@ So we have 1879/7100 (26.46%) matching already
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-10/" />
<meta property="article:published_time" content="2021-10-01T11:14:07+03:00" />
<meta property="article:modified_time" content="2021-10-04T19:40:13+03:00" />
<meta property="article:modified_time" content="2021-10-05T18:54:39+03:00" />
@ -56,9 +56,9 @@ So we have 1879/7100 (26.46%) matching already
"@type": "BlogPosting",
"headline": "October, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-10/",
"wordCount": "771",
"wordCount": "1307",
"datePublished": "2021-10-01T11:14:07+03:00",
"dateModified": "2021-10-04T19:40:13+03:00",
"dateModified": "2021-10-05T18:54:39+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -247,7 +247,71 @@ $ csvgrep -c 'number of matches' -m '0' /tmp/agrovoc-matches.csv | csvcut -c 1 &
...
Total number of bot hits purged: 465119
</code></pre><!-- raw HTML omitted -->
</code></pre><h2 id="2021-10-06">2021-10-06</h2>
<ul>
<li>Thinking about how we could check for duplicates before importing
<ul>
<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>
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= &gt; CREATE EXTENSION pg_trgm;
localhost/dspace63= &gt; 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') &gt; 0.5;
metadata_value_id │ text_value │ dspace_object_id
───────────────────┼────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
3652624 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ b7f0bf12-b183-4b2f-bbd2-7a5697b0c467
3677663 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ fb62f551-f4a5-4407-8cdc-6bff6dac399e
(2 rows)
</code></pre><ul>
<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>
<li>I started working on a basic Python script to do this and managed to find an actual duplicate in the recent IWMI items
<ul>
<li>I think I will check for similar titles, and if I find them I will print out the handles for verification</li>
<li>I could also proceed to check other metadata like type because those shouldn&rsquo;t vary too much</li>
</ul>
</li>
<li>I ran my new <code>check-duplicates.py</code> script on the 292 non-IWMI publications from Udana and found twelve potential duplicates
<ul>
<li>Upon checking them manually, I found that 7/12 were indeed already present on CGSpace!</li>
<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>
<li>I re-ran it with higher thresholds this eliminated all false positives, but it still took 24 minutes to run for 292 items!
<ul>
<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>
<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>
<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>
</ul>
</li>
</ul>
</li>
<li>Some minor updates to csv-metadata-quality
<ul>
<li>Fix two issues with regular expressions in the duplicate items and experimental language checks</li>
<li>Add a check for items that have a DOI listed in their citation, but are missing a standalone DOI field</li>
</ul>
</li>
<li>Then I ran this new version of csv-metadata-quality on an export of IWMI&rsquo;s community, minus some fields I don&rsquo;t want to check:</li>
</ul>
<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 &gt; /tmp/iwmi-to-check.csv
$ csv-metadata-quality -i /tmp/iwmi-to-check.csv -o /tmp/iwmi.csv | tee /tmp/out.log
$ xsv split -s 2000 /tmp /tmp/iwmi.csv
</code></pre><ul>
<li>I noticed each CSV only had 10 or 20 corrections, mostly that none of the duplicate metadata values were removed in the CSVs&hellip;
<ul>
<li>I cut a subset of the fields from the main CSV and tried again, but DSpace said &ldquo;no changes detected&rdquo;</li>
<li>The duplicates are definitely removed from the CSV, but DSpace doesn&rsquo;t detect them</li>
<li>I realized this is an issue I&rsquo;ve had before, but forgot because I usually use csv-metadata-quality for new items, not ones already inside DSpace!</li>
<li>I found a comment on thread on the dspace-tech mailing list from helix84 in 2015 (&ldquo;No changes were detected&rdquo; when importing metadata via XMLUI&quot;) where he says:</li>
</ul>
</li>
</ul>
<blockquote>
<p>It&rsquo;s very likely that multiple values in a single field are being compared as an unordered set rather than an ordered list.
Try doing it in two imports. In first import, remove all authors. In second import, add them in the new order.</p>
</blockquote>
<ul>
<li>Shit, so that&rsquo;s worth looking into&hellip;</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="2021-10-04T19:40:13+03:00" />
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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="2021-10-04T19:40:13+03:00" />
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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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="2021-10-04T19:40:13+03:00" />
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</url><url>
<loc>https://alanorth.github.io/cgspace-notes/2021-09/</loc>
<lastmod>2021-10-04T11:10:54+03:00</lastmod>