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@ -656,4 +656,111 @@ $ http 'http://localhost:9200/openrxv-items-final/_search?_source_includes=affil
- replace: International Livestock Research Institute
- I re-uploaded the mappings to Elasticsearch like I did yesterday and restarted the harvesting
## 2020-10-24
- Atmire sent a small version bump to CUA (6.x-4.1.10-ilri-RC5) to fix the logging of bot requests when `usage-statistics.logBots` is false
- I tested it by making several requests to DSpace Test with the `RTB website BOT` and `Delphi 2009` user agents and can verify that they are no longer logged
- I spent a few hours working on mappings on AReS
- I decided to do a full re-harvest on AReS with *no mappings* so I could extract the CRPs and affiliations to see how much work they needed
- I worked on my Python script to process some cleanups of the values to create find/replace mappings for common scenarios:
- Removing acronyms from the end of strings
- Removing "CRP on " from strings
- The problem is that the mappings are applied to all fields, and we want to keep "CGIAR Research Program on ..." in the authors, but not in the CRPs field
- Really the best solution is to have each repository use the same controlled vocabularies
## 2020-10-25
- I re-installed DSpace Test with a fresh snapshot of CGSpace's to test the DSpace 6 upgrade (the last time was in 2020-05, and we've fixed a lot of issues since then):
```
$ cp dspace/etc/postgres/update-sequences.sql /tmp/dspace5-update-sequences.sql
$ git checkout origin/6_x-dev-atmire-modules
$ chrt -b 0 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false clean package
$ sudo su - postgres
$ psql dspacetest -c 'CREATE EXTENSION pgcrypto;'
$ psql dspacetest -c "DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');"
$ exit
$ sudo systemctl stop tomcat7
$ cd dspace/target/dspace-installer
$ rm -rf /blah/dspacetest/config/spring
$ ant update
$ dspace database migrate
(10 minutes)
$ sudo systemctl start tomcat7
(discovery indexing starts)
```
- Then I started processing the Solr stats one core and 1 million records at a time:
```
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
```
- After the fifth or so run I got this error:
```
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, as I saw at this same step in 2020-05, there are some documents that have IDs that have *not* been converted to UUID, and have *not* been labeled as "unmigrated" either...
- I see there are about 217,000 of them, 99% of which are of `type: 5` which is "search"
- I purged them:
```
$ curl -s "http://localhost:8083/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</query></delete>"
```
- Then I restarted the `solr-upgrade-statistics-6x` process, which apparently had no records left to process
- I started processing the statistics-2019 core...
- I managed to process 7.5 million records in 7 hours without any errors!
## 2020-10-26
- The statistics processing on the statistics-2018 core errored after 1.8 million records:
```
Exception: Java heap space
java.lang.OutOfMemoryError: Java heap space
```
- I had the same problem when I processed the statistics-2018 core in 2020-07 and 2020-08
- I will try to purge some unmigrated records (around 460,000), most of which are of `type: 5` (search) so not relevant to our views and downloads anyways:
```console
$ curl -s "http://localhost:8083/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>id:/.+-unmigrated/</query></delete>"
```
- I restarted the process and it crashed again a few minutes later
- I increased the memory to 4096m and tried again
- It eventually completed, after which time I purge all remaining 350,000 unmigrated records (99% of which were `type: 5`):
```
$ curl -s "http://localhost:8083/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</query></delete>"
```
- Then I started processing the statistics-2017 core...
- I filed an issue with Atmire about the duplicate values in the `owningComm` and `containerCommunity` fields in Solr: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839
- Add new ORCID identifier for [Perle LATRE DE LATE](https://orcid.org/0000-0003-3871-6277) to controlled vocabulary
<!-- vim: set sw=2 ts=2: -->

122
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@ -23,7 +23,7 @@ During the FlywayDB migration I got an error:
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-10/" />
<meta property="article:published_time" content="2020-10-06T16:55:54+03:00" />
<meta property="article:modified_time" content="2020-10-22T11:58:26+03:00" />
<meta property="article:modified_time" content="2020-10-24T22:23:06+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="October, 2020"/>
@ -51,9 +51,9 @@ During the FlywayDB migration I got an error:
"@type": "BlogPosting",
"headline": "October, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-10/",
"wordCount": "4350",
"wordCount": "5014",
"datePublished": "2020-10-06T16:55:54+03:00",
"dateModified": "2020-10-22T11:58:26+03:00",
"dateModified": "2020-10-24T22:23:06+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -432,7 +432,7 @@ $ http --print Hh https://dspacetest.cgiar.org/rest/bitstreams/dfa1d9c3-75d3-438
<li>Reference: <a href="https://lucene.apache.org/core/4_0_0/queryparser/org/apache/lucene/queryparser/classic/package-summary.html#Regexp_Searches">https://lucene.apache.org/core/4_0_0/queryparser/org/apache/lucene/queryparser/classic/package-summary.html#Regexp_Searches</a></li>
</ul>
</li>
<li>I added <code>[Ss]pider</code> to the Tomcat Crawler Sessions Manager Valve regex because this can catch a few more generic bots and force them to use the same Tomcat JSESSIONID</li>
<li>I added <code>[Ss]pider</code> to the Tomcat Crawler Session Manager Valve regex because this can catch a few more generic bots and force them to use the same Tomcat JSESSIONID</li>
<li>I added a few of the patterns from above to our local agents list and ran the <code>check-spider-hits.sh</code> on CGSpace:</li>
</ul>
<pre><code>$ ./check-spider-hits.sh -f dspace/config/spiders/agents/ilri -s statistics -u http://localhost:8083/solr -p
@ -865,6 +865,120 @@ $ csvcut -c 'id,dc.subject[],dc.subject[en_US],cg.subject.ilri[],cg.subject.ilri
</li>
<li>I re-uploaded the mappings to Elasticsearch like I did yesterday and restarted the harvesting</li>
</ul>
<h2 id="2020-10-24">2020-10-24</h2>
<ul>
<li>Atmire sent a small version bump to CUA (6.x-4.1.10-ilri-RC5) to fix the logging of bot requests when <code>usage-statistics.logBots</code> is false
<ul>
<li>I tested it by making several requests to DSpace Test with the <code>RTB website BOT</code> and <code>Delphi 2009</code> user agents and can verify that they are no longer logged</li>
</ul>
</li>
<li>I spent a few hours working on mappings on AReS
<ul>
<li>I decided to do a full re-harvest on AReS with <em>no mappings</em> so I could extract the CRPs and affiliations to see how much work they needed</li>
<li>I worked on my Python script to process some cleanups of the values to create find/replace mappings for common scenarios:
<ul>
<li>Removing acronyms from the end of strings</li>
<li>Removing &ldquo;CRP on &quot; from strings</li>
</ul>
</li>
<li>The problem is that the mappings are applied to all fields, and we want to keep &ldquo;CGIAR Research Program on &hellip;&rdquo; in the authors, but not in the CRPs field</li>
<li>Really the best solution is to have each repository use the same controlled vocabularies</li>
</ul>
</li>
</ul>
<h2 id="2020-10-25">2020-10-25</h2>
<ul>
<li>I re-installed DSpace Test with a fresh snapshot of CGSpace&rsquo;s to test the DSpace 6 upgrade (the last time was in 2020-05, and we&rsquo;ve fixed a lot of issues since then):</li>
</ul>
<pre><code>$ cp dspace/etc/postgres/update-sequences.sql /tmp/dspace5-update-sequences.sql
$ git checkout origin/6_x-dev-atmire-modules
$ chrt -b 0 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false clean package
$ sudo su - postgres
$ psql dspacetest -c 'CREATE EXTENSION pgcrypto;'
$ psql dspacetest -c &quot;DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');&quot;
$ exit
$ sudo systemctl stop tomcat7
$ cd dspace/target/dspace-installer
$ rm -rf /blah/dspacetest/config/spring
$ ant update
$ dspace database migrate
(10 minutes)
$ sudo systemctl start tomcat7
(discovery indexing starts)
</code></pre><ul>
<li>Then I started processing the Solr stats one core and 1 million records at a time:</li>
</ul>
<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 1000000 -i statistics
</code></pre><ul>
<li>After the fifth or so run I got this error:</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$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>So basically, as I saw at this same step in 2020-05, there are some documents that have IDs that have <em>not</em> been converted to UUID, and have <em>not</em> been labeled as &ldquo;unmigrated&rdquo; either&hellip;
<ul>
<li>I see there are about 217,000 of them, 99% of which are of <code>type: 5</code> which is &ldquo;search&rdquo;</li>
<li>I purged them:</li>
</ul>
</li>
</ul>
<pre><code>$ curl -s &quot;http://localhost:8083/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>Then I restarted the <code>solr-upgrade-statistics-6x</code> process, which apparently had no records left to process</li>
<li>I started processing the statistics-2019 core&hellip;
<ul>
<li>I managed to process 7.5 million records in 7 hours without any errors!</li>
</ul>
</li>
</ul>
<h2 id="2020-10-26">2020-10-26</h2>
<ul>
<li>The statistics processing on the statistics-2018 core errored after 1.8 million records:</li>
</ul>
<pre><code>Exception: Java heap space
java.lang.OutOfMemoryError: Java heap space
</code></pre><ul>
<li>I had the same problem when I processed the statistics-2018 core in 2020-07 and 2020-08
<ul>
<li>I will try to purge some unmigrated records (around 460,000), most of which are of <code>type: 5</code> (search) so not relevant to our views and downloads anyways:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s &quot;http://localhost:8083/solr/statistics-2018/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary &quot;&lt;delete&gt;&lt;query&gt;id:/.+-unmigrated/&lt;/query&gt;&lt;/delete&gt;&quot;
</code></pre><ul>
<li>I restarted the process and it crashed again a few minutes later
<ul>
<li>I increased the memory to 4096m and tried again</li>
<li>It eventually completed, after which time I purge all remaining 350,000 unmigrated records (99% of which were <code>type: 5</code>):</li>
</ul>
</li>
</ul>
<pre><code>$ curl -s &quot;http://localhost:8083/solr/statistics-2018/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>Then I started processing the statistics-2017 core&hellip;</li>
<li>I filed an issue with Atmire about the duplicate values in the <code>owningComm</code> and <code>containerCommunity</code> fields in Solr: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839</a></li>
<li>Add new ORCID identifier for <a href="https://orcid.org/0000-0003-3871-6277">Perle LATRE DE LATE</a> to controlled vocabulary</li>
</ul>
<!-- raw HTML omitted -->

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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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+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/notes/" />
<meta property="og:updated_time" content="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="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/categories/notes/" />
<meta property="og:updated_time" content="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="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/categories/notes/" />
<meta property="og:updated_time" content="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="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/categories/notes/" />
<meta property="og:updated_time" content="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+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="2020-10-22T11:58:26+03:00" />
<meta property="og:updated_time" content="2020-10-24T22:23:06+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>

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