Add notes for 2018-09-30

content/posts/2018-09.md

@@ -611,4 +611,73 @@ $ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
 - It seems to be Moayad trying to do the AReS explorer indexing
 - He was sending too many (5 or 10) concurrent requests to the server, but still... why is this shit so slow?!
 
+## 2018-09-30
+
+- Valerio keeps sending items on CGSpace that have weird or incorrect languages, authors, etc
+- I think I should just batch export and update all languages...
+
+```
+dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/2018-09-30-languages.csv with csv;
+```
+
+- Then I can simply delete the "Other" and "other" ones because that's not useful at all:
+
+```
+dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='Other';
+DELETE 6
+dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='other';
+DELETE 79
+```
+
+- Looking through the list I see some weird language codes like `gh`, so I checked out those items:
+
+```
+dspace=# SELECT resource_id FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
+ resource_id
+-------------
+       94530
+       94529
+dspace=# SELECT handle,item_id FROM item, handle WHERE handle.resource_type_id=2 AND handle.resource_id = item.item_id AND handle.resource_id in (94530, 94529);
+   handle    | item_id
+-------------+---------
+ 10568/91386 |   94529
+ 10568/91387 |   94530
+```
+
+- Those items are from Ghana, so the submitter apparently thought `gh` was a language... I can safely delete them:
+
+```
+dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
+DELETE 2
+```
+
+- The next issue would be `jn`:
+
+```
+dspace=# SELECT resource_id FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jn';
+ resource_id
+-------------
+       94001
+       94003
+dspace=# SELECT handle,item_id FROM item, handle WHERE handle.resource_type_id=2 AND handle.resource_id = item.item_id AND handle.resource_id in (94001, 94003);
+   handle    | item_id
+-------------+---------
+ 10568/90868 |   94001
+ 10568/90870 |   94003
+```
+
+- Those items are about Japan, so I will update them to be `ja`
+- Other replacements:
+
+```
+DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
+UPDATE metadatavalue SET text_value='fr' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='fn';
+UPDATE metadatavalue SET text_value='hi' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='in';
+UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='Ja';
+UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jn';
+UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jp';
+```
+
+- Then there are 12 items with `en|hi`, but they were all in one collection so I just exported it as a CSV and then re-imported the corrected metadata
+
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docs/2015-11/index.html

@@ -22,6 +22,7 @@ $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspac
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2015-11/" /><meta property="article:published_time" content="2015-11-23T17:00:57&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="November, 2015"/>
 <meta name="twitter:description" content="2015-11-22
@@ -37,7 +38,7 @@ $ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspac
 
 
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docs/2015-12/index.html

@@ -23,6 +23,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2015-12/" /><meta property="article:published_time" content="2015-12-02T13:18:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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 <meta name="twitter:title" content="December, 2015"/>
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@@ -39,7 +40,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
 
 
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docs/2016-01/index.html

@@ -18,6 +18,7 @@ Update GitHub wiki for documentation of maintenance tasks.
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-01/" /><meta property="article:published_time" content="2016-01-13T13:18:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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 <meta name="twitter:title" content="January, 2016"/>
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@@ -29,7 +30,7 @@ Update GitHub wiki for documentation of maintenance tasks.
 
 
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docs/2016-02/index.html

@@ -25,6 +25,7 @@ Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE&r
 <meta property="og:type" content="article" />
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 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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 <meta name="twitter:title" content="February, 2016"/>
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@@ -43,7 +44,7 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
 
 
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docs/2016-03/index.html

@@ -18,6 +18,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
 <meta property="og:type" content="article" />
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 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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 <meta name="twitter:title" content="March, 2016"/>
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@@ -29,7 +30,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
 
 
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docs/2016-04/index.html

@@ -20,6 +20,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-04/" /><meta property="article:published_time" content="2016-04-04T11:06:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="April, 2016"/>
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@@ -33,7 +34,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
 
 
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docs/2016-05/index.html

@@ -22,6 +22,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
 <meta property="og:type" content="article" />
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 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2016"/>
 <meta name="twitter:description" content="2016-05-01
@@ -37,7 +38,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
 
 
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-<meta name="generator" content="Hugo 0.48" />
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docs/2016-06/index.html

@@ -21,6 +21,7 @@ Working on second phase of metadata migration, looks like this will work for mov
 <meta property="og:type" content="article" />
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 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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@@ -35,7 +36,7 @@ Working on second phase of metadata migration, looks like this will work for mov
 
 
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docs/2016-07/index.html

@@ -29,6 +29,7 @@ In this case the select query was showing 95 results before the update
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-07/" /><meta property="article:published_time" content="2016-07-01T10:53:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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 <meta name="twitter:title" content="July, 2016"/>
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@@ -51,7 +52,7 @@ In this case the select query was showing 95 results before the update
 
 
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docs/2016-08/index.html

@@ -26,6 +26,7 @@ $ git rebase -i dspace-5.5
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-08/" /><meta property="article:published_time" content="2016-08-01T15:53:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="August, 2016"/>
 <meta name="twitter:description" content="2016-08-01
@@ -45,7 +46,7 @@ $ git rebase -i dspace-5.5
 
 
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docs/2016-09/index.html

@@ -22,6 +22,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=or
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-09/" /><meta property="article:published_time" content="2016-09-01T15:53:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="September, 2016"/>
 <meta name="twitter:description" content="2016-09-01
@@ -37,7 +38,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
 
 
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-<meta name="generator" content="Hugo 0.48" />
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docs/2016-10/index.html

@@ -26,6 +26,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-10/" /><meta property="article:published_time" content="2016-10-03T15:53:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-04-04T16:25:57&#43;03:00"/>
+
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="October, 2016"/>
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@@ -45,7 +46,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
 
 
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docs/2016-11/index.html

@@ -18,6 +18,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module
 <meta property="og:type" content="article" />
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 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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 <meta name="twitter:title" content="November, 2016"/>
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@@ -29,7 +30,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
 
 
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docs/2016-12/index.html

@@ -30,6 +30,7 @@ Another worrying error from dspace.log is:
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-12/" /><meta property="article:published_time" content="2016-12-02T10:43:00&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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@@ -53,7 +54,7 @@ Another worrying error from dspace.log is:
 
 
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docs/2017-01/index.html

@@ -18,6 +18,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
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+
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@@ -29,7 +30,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
 
 
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docs/2017-02/index.html

@@ -32,6 +32,7 @@ Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name
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+
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@@ -57,7 +58,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
 
 
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docs/2017-03/index.html

@@ -34,6 +34,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
 <meta property="og:type" content="article" />
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+
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@@ -61,7 +62,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
 
 
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docs/2017-04/index.html

@@ -27,6 +27,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Th
 <meta property="og:type" content="article" />
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+
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@@ -47,7 +48,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
 
 
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docs/2017-05/index.html

@@ -10,10 +10,11 @@
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-05/" /><meta property="article:published_time" content="2017-05-01T16:21:52&#43;02:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2017"/>
 <meta name="twitter:description" content="2017-05-01  ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items:  https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683   2017-05-02  Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request  2017-05-04  Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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docs/2017-06/index.html

@@ -10,10 +10,11 @@
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-06/" /><meta property="article:published_time" content="2017-06-01T10:14:52&#43;03:00"/>
 <meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+
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 <meta name="twitter:title" content="June, 2017"/>
 <meta name="twitter:description" content="2017-06-01  After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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docs/2017-07/index.html

@@ -24,6 +24,7 @@ We can use PostgreSQL’s extended output format (-x) plus sed to format the
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docs/2017-08/index.html

@@ -34,6 +34,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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+
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@@ -61,7 +62,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
 
 
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docs/2017-09/index.html

@@ -22,6 +22,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account
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docs/2017-10/index.html

@@ -24,6 +24,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
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@@ -16,6 +16,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
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@@ -41,9 +42,9 @@ I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I
   "@type": "BlogPosting",
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   "url": "https://alanorth.github.io/cgspace-notes/2018-09/",
-  "wordCount": "4757",
+  "wordCount": "5245",
   "datePublished": "2018-09-02T09:55:54&#43;03:00",
-  "dateModified": "2018-09-29T15:00:03&#43;03:00",
+  "dateModified": "2018-09-29T19:00:41&#43;03:00",
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     "@type": "Person",
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@@ -812,6 +813,83 @@ $ ./fix-metadata-values.py -i 2018-09-29-fix-authors.csv -db dspace -u dspace -p
 <li>He was sending too many (5 or 10) concurrent requests to the server, but still&hellip; why is this shit so slow?!</li>
 </ul>
 
+<h2 id="2018-09-30">2018-09-30</h2>
+
+<ul>
+<li>Valerio keeps sending items on CGSpace that have weird or incorrect languages, authors, etc</li>
+<li>I think I should just batch export and update all languages&hellip;</li>
+</ul>
+
+<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/2018-09-30-languages.csv with csv;
+</code></pre>
+
+<ul>
+<li>Then I can simply delete the &ldquo;Other&rdquo; and &ldquo;other&rdquo; ones because that&rsquo;s not useful at all:</li>
+</ul>
+
+<pre><code>dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='Other';
+DELETE 6
+dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='other';
+DELETE 79
+</code></pre>
+
+<ul>
+<li>Looking through the list I see some weird language codes like <code>gh</code>, so I checked out those items:</li>
+</ul>
+
+<pre><code>dspace=# SELECT resource_id FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
+ resource_id
+-------------
+       94530
+       94529
+dspace=# SELECT handle,item_id FROM item, handle WHERE handle.resource_type_id=2 AND handle.resource_id = item.item_id AND handle.resource_id in (94530, 94529);
+   handle    | item_id
+-------------+---------
+ 10568/91386 |   94529
+ 10568/91387 |   94530
+</code></pre>
+
+<ul>
+<li>Those items are from Ghana, so the submitter apparently thought <code>gh</code> was a language&hellip; I can safely delete them:</li>
+</ul>
+
+<pre><code>dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
+DELETE 2
+</code></pre>
+
+<ul>
+<li>The next issue would be <code>jn</code>:</li>
+</ul>
+
+<pre><code>dspace=# SELECT resource_id FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jn';
+ resource_id
+-------------
+       94001
+       94003
+dspace=# SELECT handle,item_id FROM item, handle WHERE handle.resource_type_id=2 AND handle.resource_id = item.item_id AND handle.resource_id in (94001, 94003);
+   handle    | item_id
+-------------+---------
+ 10568/90868 |   94001
+ 10568/90870 |   94003
+</code></pre>
+
+<ul>
+<li>Those items are about Japan, so I will update them to be <code>ja</code></li>
+<li>Other replacements:</li>
+</ul>
+
+<pre><code>DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='gh';
+UPDATE metadatavalue SET text_value='fr' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='fn';
+UPDATE metadatavalue SET text_value='hi' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='in';
+UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='Ja';
+UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jn';
+UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'language' and qualifier = 'iso') AND text_value='jp';
+</code></pre>
+
+<ul>
+<li>Then there are 12 items with <code>en|hi</code>, but they were all in one collection so I just exported it as a CSV and then re-imported the corrected metadata</li>
+</ul>
+
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