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Code Issues Projects Releases Wiki Activity

Update notes for 2020-05-31

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Alan Orth 2020-05-31 20:49:41 +03:00
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26 changed files with 119 additions and 36 deletions
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45
content/posts/2020-05.md
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@ -216,10 +216,53 @@ $ ant update
- Database migrations take 10:18.287s during the first startup...
- perhaps when we do the production CGSpace migration I can do this in advance and tell users not to make any submissions?
- I had a mistake in my Solr internal URL parameter so DSpace couldn't find it, but once I fixed that DSpace starts up OK!
- Once the initial Discovery reindexing is completed I started the Solr statistics UUID migration:
- Once the initial Discovery reindexing was completed (after three hours or so!) I started the Solr statistics UUID migration:
```
$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
$ dspace solr-upgrade-statistics-6x -i statistics -n 250000
$ dspace solr-upgrade-statistics-6x -i statistics -n 1000000
$ dspace solr-upgrade-statistics-6x -i statistics -n 1000000
...
```
- It's taking about 35 minutes for 1,000,000 records...
- Some issues towards the end of this core:
```
Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
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)
```
- So basically there are some documents that have IDs that have *not* been converted to UUID, and have *not* been labeled as "unmigrated" either...
- Of these 101,257 documents, 90,000 are of type 5 (search), 9,000 are type storage, and 800 are type view, but it's weird because if I look at their type/statistics_type using a facet the storage ones disappear...
- For now I will export these documents from the statistics core and then delete them:
```
$ ./run.sh -s http://localhost:8081/solr/statistics -a export -o statistics-unmigrated.json -k uid -f '(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)'
$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</query></delete>"
```
- Now the UUID conversion script says there is nothing left to convert, so I can try to run the Atmire CUA conversion utility:
```
$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
$ dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 1
```
- Experiment a bit with the Python [country-converter](https://pypi.org/project/country-converter/) library as it can convert between different formats (like ISO 3166 and UN m49)

6
docs/2020-04/index.html
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@ -25,7 +25,7 @@ On the same note, the one item Abenet pointed out last week now has a donut with
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-04/" />
<meta property="article:published_time" content="2020-04-02T10:53:24+03:00" />
<meta property="article:modified_time" content="2020-04-30T14:49:46+03:00" />
<meta property="article:modified_time" content="2020-05-31T20:15:08+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="April, 2020"/>
@ -57,7 +57,7 @@ On the same note, the one item Abenet pointed out last week now has a donut with
"url": "https://alanorth.github.io/cgspace-notes/2020-04/",
"wordCount": "3406",
"datePublished": "2020-04-02T10:53:24+03:00",
"dateModified": "2020-04-30T14:49:46+03:00",
"dateModified": "2020-05-31T20:15:08+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -454,7 +454,7 @@ atmire-cua.version.number=${cua.version.number}
</li>
</ul>
</li>
<li>I manually editied the CUA version variable and was then able to run the <code>com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI</code> script
<li>I manually edited the CUA version variable and was then able to run the <code>com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI</code> script
<ul>
<li>On the first run it took one hour to process 100,000 records on my local test instance&hellip;</li>
<li>On the second run it took one hour to process 140,000 records</li>

48
docs/2020-05/index.html
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@ -18,7 +18,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-05/" />
<meta property="article:published_time" content="2020-05-02T09:52:04+03:00" />
<meta property="article:modified_time" content="2020-05-30T18:38:16+03:00" />
<meta property="article:modified_time" content="2020-05-31T16:04:18+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2020"/>
@ -41,9 +41,9 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
"@type": "BlogPosting",
"headline": "May, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-05/",
"wordCount": "1861",
"wordCount": "2094",
"datePublished": "2020-05-02T09:52:04+03:00",
"dateModified": "2020-05-30T18:38:16+03:00",
"dateModified": "2020-05-31T16:04:18+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -386,9 +386,49 @@ $ ant update
</ul>
</li>
<li>I had a mistake in my Solr internal URL parameter so DSpace couldn&rsquo;t find it, but once I fixed that DSpace starts up OK!</li>
<li>Once the initial Discovery reindexing is completed I started the Solr statistics UUID migration:</li>
<li>Once the initial Discovery reindexing was completed (after three hours or so!) I started the Solr statistics UUID migration:</li>
</ul>
<pre><code>$ export JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot;
$ dspace solr-upgrade-statistics-6x -i statistics -n 250000
$ dspace solr-upgrade-statistics-6x -i statistics -n 1000000
$ dspace solr-upgrade-statistics-6x -i statistics -n 1000000
...
</code></pre><ul>
<li>It&rsquo;s taking about 35 minutes for 1,000,000 records&hellip;</li>
<li>Some issues towards the end of this core:</li>
</ul>
<pre><code>Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>So basically there are some documents that have IDs that have <em>not</em> been converted to UUID, and have <em>not</em> been labeled as &ldquo;unmigrated&rdquo; either&hellip;
<ul>
<li>Of these 101,257 documents, 90,000 are of type 5 (search), 9,000 are type storage, and 800 are type view, but it&rsquo;s weird because if I look at their type/statistics_type using a facet the storage ones disappear&hellip;</li>
<li>For now I will export these documents from the statistics core and then delete them:</li>
</ul>
</li>
</ul>
<pre><code>$ ./run.sh -s http://localhost:8081/solr/statistics -a export -o statistics-unmigrated.json -k uid -f '(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)'
$ curl -s &quot;http://localhost:8081/solr/statistics/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary &quot;&lt;delete&gt;&lt;query&gt;(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)&lt;/query&gt;&lt;/delete&gt;&quot;
</code></pre><ul>
<li>Now the UUID conversion script says there is nothing left to convert, so I can try to run the Atmire CUA conversion utility:</li>
</ul>
<pre><code>$ export JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot;
$ dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 1
</code></pre><ul>
<li>Experiment a bit with the Python <a href="https://pypi.org/project/country-converter/">country-converter</a> library as it can convert between different formats (like ISO 3166 and UN m49)
<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="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>

2
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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="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>

2
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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="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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/" />
<meta property="og:updated_time" content="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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/" />
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<meta property="og:updated_time" content="2020-05-31T20:15:08+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/" />
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<meta property="og:updated_time" content="2020-05-31T20:15:08+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>

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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="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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/" />
<meta property="og:updated_time" content="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>

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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="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-05-30T18:38:16+03:00" />
<meta property="og:updated_time" content="2020-05-31T20:15:08+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" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<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 name="twitter:title" content="CGSpace Notes"/>

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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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