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Add notes for 2020-12-17

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Alan Orth 2020-12-17 16:50:56 +02:00
parent 29fbe6555f
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23 changed files with 136 additions and 29 deletions
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55
content/posts/2020-12.md
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@ -480,4 +480,59 @@ $ grep -o -E 'by .*)' /tmp/provenance.txt | grep -v -E "( on |checksum)" | sed -
- Peter wanted it to send some mail to the users...
## 2020-12-17
- I see some errors from CUA in our Tomcat logs:
```console
Thu Dec 17 07:35:27 CET 2020 | Query:containerItem:b049326a-0e76-45a8-ac0c-d8ec043a50c6
Error while updating
java.lang.UnsupportedOperationException: Multiple update components target the same field:solr_update_time_stamp
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1155)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:241)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1140)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1129)
...
```
- I sent the full stack to Atmire to investigate
- I know we've had thisi "Multiple update components target the same field" error in the past with DSpace 5.x and Atmire said it was harmless, but would nevertheless be fixed in a future update
- I was trying to export the ILRI community on CGSpace so I could update one of the ILRI author's names, but it throws an error...
```console
$ dspace metadata-export -i 10568/1 -f /tmp/2020-12-17-ILRI.csv
Loading @mire database changes for module MQM
Changes have been processed
Exporting community 'International Livestock Research Institute (ILRI)' (10568/1)
Exception: null
java.lang.NullPointerException
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:212)
at com.google.common.collect.Iterators.concat(Iterators.java:464)
at org.dspace.app.bulkedit.MetadataExport.addItemsToResult(MetadataExport.java:136)
at org.dspace.app.bulkedit.MetadataExport.buildFromCommunity(MetadataExport.java:125)
at org.dspace.app.bulkedit.MetadataExport.<init>(MetadataExport.java:77)
at org.dspace.app.bulkedit.MetadataExport.main(MetadataExport.java:282)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
```
- I did it via CSV with `fix-metadata-values.py` instead:
```console
$ cat 2020-12-17-update-ILRI-author.csv
dc.contributor.author,correct
"Padmakumar, V.P.","Varijakshapanicker, Padmakumar"
$ ./fix-metadata-values.py -i 2020-12-17-update-ILRI-author.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3
- Abenet needed a list of all 2020 outputs from the Livestock CRP that were Limited Access
- I exported the community from CGSpace and used `csvcut` and `csvgrep` to get a list:
```
$ csvcut -c 'dc.identifier.citation[en_US],dc.identifier.uri,dc.identifier.uri[],dc.identifier.uri[en_US],dc.date.issued,dc.date.issued[],dc.date.issued[en_US],cg.identifier.status[en_US]' ~/Downloads/10568-80099.csv | csvgrep -c 'cg.identifier.status[en_US]' -m 'Limited Access' | csvgrep -c 'dc.date.issued' -m 2020 -c 'dc.date.issued[]' -m 2020 -c 'dc.date.issued[en_US]' -m 2020 > /tmp/limited-2020.csv
```
<!-- vim: set sw=2 ts=2: -->

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@ -20,7 +20,7 @@ I started processing those (about 411,000 records):
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-12/" />
<meta property="article:published_time" content="2020-12-01T11:32:54+02:00" />
<meta property="article:modified_time" content="2020-12-16T09:54:40+02:00" />
<meta property="article:modified_time" content="2020-12-16T12:08:00+02:00" />
@ -46,9 +46,9 @@ I started processing those (about 411,000 records):
"@type": "BlogPosting",
"headline": "December, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-12/",
"wordCount": "2711",
"wordCount": "2970",
"datePublished": "2020-12-01T11:32:54+02:00",
"dateModified": "2020-12-16T09:54:40+02:00",
"dateModified": "2020-12-16T12:08:00+02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -616,7 +616,59 @@ $ grep -o -E 'by .*)' /tmp/provenance.txt | grep -v -E &quot;( on |checksum)&quo
</code></pre><ul>
<li>Peter wanted it to send some mail to the users&hellip;</li>
</ul>
<!-- raw HTML omitted -->
<h2 id="2020-12-17">2020-12-17</h2>
<ul>
<li>I see some errors from CUA in our Tomcat logs:</li>
</ul>
<pre><code class="language-console" data-lang="console">Thu Dec 17 07:35:27 CET 2020 | Query:containerItem:b049326a-0e76-45a8-ac0c-d8ec043a50c6
Error while updating
java.lang.UnsupportedOperationException: Multiple update components target the same field:solr_update_time_stamp
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1155)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:241)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1140)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1129)
...
</code></pre><ul>
<li>I sent the full stack to Atmire to investigate
<ul>
<li>I know we&rsquo;ve had thisi &ldquo;Multiple update components target the same field&rdquo; error in the past with DSpace 5.x and Atmire said it was harmless, but would nevertheless be fixed in a future update</li>
</ul>
</li>
<li>I was trying to export the ILRI community on CGSpace so I could update one of the ILRI author&rsquo;s names, but it throws an error&hellip;</li>
</ul>
<pre><code class="language-console" data-lang="console">$ dspace metadata-export -i 10568/1 -f /tmp/2020-12-17-ILRI.csv
Loading @mire database changes for module MQM
Changes have been processed
Exporting community 'International Livestock Research Institute (ILRI)' (10568/1)
Exception: null
java.lang.NullPointerException
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:212)
at com.google.common.collect.Iterators.concat(Iterators.java:464)
at org.dspace.app.bulkedit.MetadataExport.addItemsToResult(MetadataExport.java:136)
at org.dspace.app.bulkedit.MetadataExport.buildFromCommunity(MetadataExport.java:125)
at org.dspace.app.bulkedit.MetadataExport.&lt;init&gt;(MetadataExport.java:77)
at org.dspace.app.bulkedit.MetadataExport.main(MetadataExport.java:282)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>I did it via CSV with <code>fix-metadata-values.py</code> instead:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ cat 2020-12-17-update-ILRI-author.csv
dc.contributor.author,correct
&quot;Padmakumar, V.P.&quot;,&quot;Varijakshapanicker, Padmakumar&quot;
$ ./fix-metadata-values.py -i 2020-12-17-update-ILRI-author.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3
- Abenet needed a list of all 2020 outputs from the Livestock CRP that were Limited Access
- I exported the community from CGSpace and used `csvcut` and `csvgrep` to get a list:
</code></pre><p>$ csvcut -c &lsquo;dc.identifier.citation[en_US],dc.identifier.uri,dc.identifier.uri[],dc.identifier.uri[en_US],dc.date.issued,dc.date.issued[],dc.date.issued[en_US],cg.identifier.status[en_US]&rsquo; ~/Downloads/10568-80099.csv | csvgrep -c &lsquo;cg.identifier.status[en_US]&rsquo; -m &lsquo;Limited Access&rsquo; | csvgrep -c &lsquo;dc.date.issued&rsquo; -m 2020 -c &lsquo;dc.date.issued[]&rsquo; -m 2020 -c &lsquo;dc.date.issued[en_US]&rsquo; -m 2020 &gt; /tmp/limited-2020.csv</p>
<pre><code>
&lt;!-- vim: set sw=2 ts=2: --&gt;
</code></pre>

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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/categories/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+02:00" />
<meta property="og:updated_time" content="2020-12-16T12:08:00+02:00" />

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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/categories/notes/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+02:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+02:00" />
<meta property="og:updated_time" content="2020-12-16T12:08:00+02:00" />

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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+02:00" />
<meta property="og:updated_time" content="2020-12-16T12:08:00+02:00" />

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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+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/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+02:00" />
<meta property="og:updated_time" content="2020-12-16T12:08:00+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/" />
<meta property="og:updated_time" content="2020-12-16T09:54:40+02:00" />
<meta property="og:updated_time" content="2020-12-16T12:08:00+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:updated_time" content="2020-12-16T09:54:40+02:00" />
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