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Add notes for 2020-08-14

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Alan Orth 2020-08-14 11:22:16 +03:00
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content/posts/2020-08.md
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@ -398,4 +398,56 @@ dspace=# SELECT count(text_value) FROM metadatavalue WHERE metadata_field_id = 2
- I purged 150,000 hits from 2020 and 2020 from these user agents and hosts
## 2020-08-14
- Last night I started the processing of the statistics-2016 core with the Atmire stats util and I see some errors like this:
```
Record uid: f6b288d7-d60d-4df9-b311-1696b88552a0 couldn't be processed
com.atmire.statistics.util.update.atomic.ProcessingException: something went wrong while processing record uid: f6b288d7-d60d-4df9-b311-1696b88552a0, an error occured in the com.atmire.statistics.util.update.atomic.processor.ContainerOwnerDBProcessor
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.applyProcessors(SourceFile:304)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.processRecords(SourceFile:176)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:161)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.update(SourceFile:128)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI.main(SourceFile:78)
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)
Caused by: java.lang.NullPointerException
```
- I see it has `id: 980-unmigrated` and `type: 0`...
- The 2016 core has 629,983 unmigrated docs, mostly:
- `type: 5`: 620311
- `type: 0`: 7255
- `type: 3`: 1333
- I purged the unmigrated docs and continued processing:
```
$ curl -s "http://localhost:8081/solr/statistics-2016/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:/.*unmigrated.*/</query></delete>'
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2016
```
- Then I see there are 849,000 docs with `id: -1` and `type: 5` so I should purge those too probably:
```
$ curl -s "http://localhost:8081/solr/statistics-2017/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:\-1</query></delete>'
```
- Altmetric asked for a dump of CGSpace's OAI "sets" so they can update their affiliation mappings
- I did it in a kinda ghetto way:
```
$ http 'https://cgspace.cgiar.org/oai/request?verb=ListSets' > /tmp/0.xml
$ for num in {100..1300..100}; do http "https://cgspace.cgiar.org/oai/request?verb=ListSets&resumptionToken=////$num" > /tmp/$num.xml; sleep 2; done
$ for num in {0..1300..100}; do cat /tmp/$num.xml >> /tmp/cgspace-oai-sets.xml; done
```
- This produces one file that has all the sets, albeit with 14 pages of responses concatenated into one document, but that's how theirs was in the first place...
- Help Bizu with a restricted item for CIAT
<!-- vim: set sw=2 ts=2: -->

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@ -19,7 +19,7 @@ It is class based so I can easily add support for other vocabularies, and the te
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-08/" />
<meta property="article:published_time" content="2020-08-02T15:35:54+03:00" />
<meta property="article:modified_time" content="2020-08-11T11:35:05+03:00" />
<meta property="article:modified_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="August, 2020"/>
@ -43,9 +43,9 @@ It is class based so I can easily add support for other vocabularies, and the te
"@type": "BlogPosting",
"headline": "August, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-08/",
"wordCount": "2554",
"wordCount": "2800",
"datePublished": "2020-08-02T15:35:54+03:00",
"dateModified": "2020-08-11T11:35:05+03:00",
"dateModified": "2020-08-13T17:56:39+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -566,6 +566,56 @@ $ curl -s &quot;http://localhost:8081/solr/statistics-2010/update?softCommit=tru
<ul>
<li>I purged 150,000 hits from 2020 and 2020 from these user agents and hosts</li>
</ul>
<h2 id="2020-08-14">2020-08-14</h2>
<ul>
<li>Last night I started the processing of the statistics-2016 core with the Atmire stats util and I see some errors like this:</li>
</ul>
<pre><code>Record uid: f6b288d7-d60d-4df9-b311-1696b88552a0 couldn't be processed
com.atmire.statistics.util.update.atomic.ProcessingException: something went wrong while processing record uid: f6b288d7-d60d-4df9-b311-1696b88552a0, an error occured in the com.atmire.statistics.util.update.atomic.processor.ContainerOwnerDBProcessor
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.applyProcessors(SourceFile:304)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.processRecords(SourceFile:176)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:161)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.update(SourceFile:128)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI.main(SourceFile:78)
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)
Caused by: java.lang.NullPointerException
</code></pre><ul>
<li>I see it has <code>id: 980-unmigrated</code> and <code>type: 0</code>&hellip;</li>
<li>The 2016 core has 629,983 unmigrated docs, mostly:
<ul>
<li><code>type: 5</code>: 620311</li>
<li><code>type: 0</code>: 7255</li>
<li><code>type: 3</code>: 1333</li>
</ul>
</li>
<li>I purged the unmigrated docs and continued processing:</li>
</ul>
<pre><code>$ curl -s &quot;http://localhost:8081/solr/statistics-2016/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary '&lt;delete&gt;&lt;query&gt;id:/.*unmigrated.*/&lt;/query&gt;&lt;/delete&gt;'
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2016
</code></pre><ul>
<li>Then I see there are 849,000 docs with <code>id: -1</code> and <code>type: 5</code> so I should purge those too probably:</li>
</ul>
<pre><code>$ curl -s &quot;http://localhost:8081/solr/statistics-2017/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary '&lt;delete&gt;&lt;query&gt;id:\-1&lt;/query&gt;&lt;/delete&gt;'
</code></pre><ul>
<li>Altmetric asked for a dump of CGSpace&rsquo;s OAI &ldquo;sets&rdquo; so they can update their affiliation mappings
<ul>
<li>I did it in a kinda ghetto way:</li>
</ul>
</li>
</ul>
<pre><code>$ http 'https://cgspace.cgiar.org/oai/request?verb=ListSets' &gt; /tmp/0.xml
$ for num in {100..1300..100}; do http &quot;https://cgspace.cgiar.org/oai/request?verb=ListSets&amp;resumptionToken=////$num&quot; &gt; /tmp/$num.xml; sleep 2; done
$ for num in {0..1300..100}; do cat /tmp/$num.xml &gt;&gt; /tmp/cgspace-oai-sets.xml; done
</code></pre><ul>
<li>This produces one file that has all the sets, albeit with 14 pages of responses concatenated into one document, but that&rsquo;s how theirs was in the first place&hellip;</li>
<li>Help Bizu with a restricted item for CIAT</li>
</ul>
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@ -9,7 +9,7 @@
<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="2020-08-11T11:35:05+03:00" />
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>

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@ -9,7 +9,7 @@
<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="2020-08-11T11:35:05+03:00" />
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>

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@ -9,7 +9,7 @@
<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="2020-08-11T11:35:05+03:00" />
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>

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@ -9,7 +9,7 @@
<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="2020-08-11T11:35:05+03:00" />
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>

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@ -9,7 +9,7 @@
<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="2020-08-11T11:35:05+03:00" />
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>

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@ -9,7 +9,7 @@
<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/" />
<meta property="og:updated_time" content="2020-08-11T11:35:05+03:00" />
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>

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@ -9,7 +9,7 @@
<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/" />
<meta property="og:updated_time" content="2020-08-11T11:35:05+03:00" />
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>

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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:updated_time" content="2020-08-13T17:56:39+03:00" />
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<meta name="twitter:title" content="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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@ -4,27 +4,27 @@
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