mirror of
https://github.com/alanorth/cgspace-notes.git
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Add notes for 2020-11-17
This commit is contained in:
@ -259,4 +259,97 @@ org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error whil
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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```
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## 2020-11-16
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- Users are having issues submitting items to CGSpace
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- Looking at the data I see that connections skyrocketed since DSpace 6 upgrade yesterday, and they are all in "waiting for lock" state:
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- There are almost 1,500 locks:
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```
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$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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1494
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```
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- I sent a mail to the dspace-tech mailing list to ask for help...
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- For now I just restarted PostgreSQL and a few users were able to complete submissions...
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- While processing the statistics-2018 Solr core I got the *same* memory error that I have gotten every time I processed this core in testing:
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```
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Exception: Java heap space
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java.lang.OutOfMemoryError: Java heap space
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at java.util.Arrays.copyOf(Arrays.java:3332)
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at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:124)
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at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:448)
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at java.lang.StringBuffer.append(StringBuffer.java:270)
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at java.io.StringWriter.write(StringWriter.java:101)
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at org.apache.solr.common.util.XML.writeXML(XML.java:133)
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at org.apache.solr.client.solrj.util.ClientUtils.writeVal(SourceFile:160)
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at org.apache.solr.client.solrj.util.ClientUtils.writeXML(SourceFile:128)
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at org.apache.solr.client.solrj.request.UpdateRequest.writeXML(UpdateRequest.java:365)
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at org.apache.solr.client.solrj.request.UpdateRequest.getXML(UpdateRequest.java:281)
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at org.apache.solr.client.solrj.request.RequestWriter.getContentStream(RequestWriter.java:67)
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at org.apache.solr.client.solrj.request.RequestWriter$LazyContentStream.getDelegate(RequestWriter.java:95)
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at org.apache.solr.client.solrj.request.RequestWriter$LazyContentStream.getName(RequestWriter.java:105)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.createMethod(HttpSolrServer.java:302)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
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at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
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at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
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at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
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at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
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at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
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at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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```
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- I increased the Java heap memory to 4096MB and restarted the processing
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- After a few hours I got the following error, which I have gotten several times over the last few months:
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```
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Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
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org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
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at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
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at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
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at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
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at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
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at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
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at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
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at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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```
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## 2020-11-17
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- Chat with Peter about using some remaining CRP Livestock open access money to fund more work on OpenRXV / AReS
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- I will create GitHub issues for each of the things we talked about and then create ToRs to send to CodeObia for a quote
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- Continue migrating Solr statistics to DSpace 6 UUID format after the upgrade on Sunday
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- Regarding the IWMI issue about flagships and strategic priorities we can use CRP Livestock as an example because all their [flagships are mapped to collections](https://cgspace.cgiar.org/handle/10568/80102)
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- Database issues are worse today...
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- There are over 2,000 locks:
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```
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$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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2071
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```
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<!-- vim: set sw=2 ts=2: -->
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294
content/posts/cgspace-dspace6-upgrade.md
Normal file
294
content/posts/cgspace-dspace6-upgrade.md
Normal file
@ -0,0 +1,294 @@
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+++
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title = "CGSpace DSpace 6 Upgrade"
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date = 2020-11-15T13:27:35+02:00
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description = "Documenting the DSpace 6 upgrade."
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categories = ["Notes"]
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tags = ["Migration"]
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url = "cgspace-dspace6-upgrade"
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+++
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Notes about the DSpace 6 upgrade on CGSpace in 2020-11.
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<!--more-->
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- [Processing Solr Statistics With solr-upgrade-statistics-6x](#processing-solr-statistics-with-solr-upgrade-statistics-6x)
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- [Current year's statistics core](#statistics)
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- [statistics-2019 core](#statistics-2019)
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- [statistics-2018 core](#statistics-2018)
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- [statistics-2017 core](#statistics-2017)
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- [statistics-2016 core](#statistics-2016)
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- [statistics-2015 core](#statistics-2015)
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- [statistics-2014 core](#statistics-2014)
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- [statistics-2013 core](#statistics-2013)
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## Processing Solr Statistics With solr-upgrade-statistics-6x
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After the main upgrade process was finished and DSpace was running I started processing the Solr statistics with `solr-upgrade-statistics-6x` to migrate all IDs to UUIDs.
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### statistics
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First process the current year's statistics core:
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```console
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$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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3,817,407 Bistream View
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1,693,443 Item View
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105,974 Collection View
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62,383 Community View
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163,192 Community Search
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162,581 Collection Search
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470,288 Unexpected Type & Full Site
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--------------------------------------
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6,475,268 TOTAL
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=================================================================
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```
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After several rounds of processing it finished. Here are some statistics about unmigrated documents:
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- 227,000: `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 471,000: `id:/.+-unmigrated/`
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- 698,000: `*:* NOT id:/.{36}/`
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- Majority are `type: 5` (aka SITE, according to `Constants.java`) so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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```
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### statistics-2019
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Processing the statistics-2019 core:
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```console
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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5,569,344 Bistream View
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2,179,105 Item View
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117,194 Community View
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104,091 Collection View
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774,138 Community Search
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568,347 Collection Search
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1,482,620 Unexpected Type & Full Site
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--------------------------------------
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10,794,839 TOTAL
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=================================================================
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```
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After several rounds of processing it finished. Here are some statistics about unmigrated documents:
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- 2,690,309: `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 1,494,587: `id:/.+-unmigrated/`
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- 4,184,896: `*:* NOT id:/.{36}/`
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- 4,172,929 are `type: 5` (aka SITE) so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics-2019/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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```
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### statistics-2018
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Processing the statistics-2018 core:
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```console
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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3,561,532 Bistream View
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1,129,326 Item View
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97,401 Community View
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63,508 Collection View
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207,827 Community Search
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43,752 Collection Search
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457,820 Unexpected Type & Full Site
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--------------------------------------
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5,561,166 TOTAL
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=================================================================
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```
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After some time I got an error about Java heap space so I increased the JVM memory and restarted processing:
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```console
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$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx4096m'
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
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```
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Eventually the processing finished. Here are some statistics about unmigrated documents:
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- 365,473: `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 546,955: `id:/.+-unmigrated/`
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- 923,158: `*:* NOT id:/.{36}/`
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- 823,293: are `type: 5` so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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```
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## statistics-2017
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Processing the statistics-2017 core:
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```console
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2017
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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2,529,208 Bistream View
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1,618,717 Item View
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144,945 Community View
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74,249 Collection View
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479,647 Community Search
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114,658 Collection Search
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852,215 Unexpected Type & Full Site
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--------------------------------------
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5,813,639 TOTAL
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=================================================================
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```
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Eventually the processing finished. Here are some statistics about unmigrated documents:
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- 808,309: `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 893,868: `id:/.+-unmigrated/`
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- 1,702,177: `*:* NOT id:/.{36}/`
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- 1,660,524 are `type: 5` (SITE) so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics-2017/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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```
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### statistics-2016
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Processing the statistics-2016 core:
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```console
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2016
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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1,765,924 Bistream View
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1,151,575 Item View
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187,110 Community View
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51,204 Collection View
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347,382 Community Search
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66,605 Collection Search
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620,298 Unexpected Type & Full Site
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--------------------------------------
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4,190,098 TOTAL
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=================================================================
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```
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- 849,408: `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 627,747: `id:/.+-unmigrated/`
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- 1,477,155: `*:* NOT id:/.{36}/`
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- 1,469,706 are `type: 5` (SITE) so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics-2016/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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```
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### statistics-2015
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Processing the statistics-2015 core:
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```console
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2015
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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990,916 Bistream View
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506,070 Item View
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116,153 Community View
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33,282 Collection View
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21,062 Community Search
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10,788 Collection Search
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52,107 Unexpected Type & Full Site
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--------------------------------------
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1,730,378 TOTAL
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=================================================================
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```
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Summary of stats after processing:
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- 195,293: `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 67,146: `id:/.+-unmigrated/`
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- 262,439: `*:* NOT id:/.{36}/`
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- 247,400 are `type: 5` (SITE) so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics-2015/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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```
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## statistics-2014
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Processing the statistics-2014 core:
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```console
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2014
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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2,381,603 Item View
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1,323,357 Bistream View
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501,545 Community View
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247,805 Collection View
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250 Collection Search
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188 Community Search
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50 Item Search
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10,918 Unexpected Type & Full Site
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--------------------------------------
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4,465,716 TOTAL
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=================================================================
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```
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Summary of unmigrated documents after processing:
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- 182,131: `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 39,947: `id:/.+-unmigrated/`
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- 222,078: `*:* NOT id:/.{36}/`
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- 188,791 are `type: 5` (SITE) so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics-2014/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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```
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## statistics-2013
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Processing the statistics-2013 core:
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```console
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2013
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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2,352,124 Item View
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1,117,676 Bistream View
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575,711 Community View
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171,639 Collection View
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248 Item Search
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7 Collection Search
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5 Community Search
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1,452 Unexpected Type & Full Site
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--------------------------------------
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4,218,862 TOTAL
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=================================================================
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```
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Summary of unmigrated docs after processing:
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- 2,548 : `(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)`
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- 29,772: `id:/.+-unmigrated/`
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- 32,320: `*:* NOT id:/.{36}/`
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- 15,691 are `type: 5` (SITE) so we can purge them:
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```console
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$ curl -s "http://localhost:8081/solr/statistics-2013/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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||||
```
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Reference in New Issue
Block a user