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---
title: "December, 2020"
date: 2020-12-01T11:32:54+02:00
author: "Alan Orth"
categories: ["Notes"]
---
## 2020-12-01
- Atmire responded about the issue with duplicate data in our Solr statistics
- They noticed that some records in the statistics-2015 core haven't been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven't migrated any of the records yet
- That's strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the `cua_version` field
- I started processing those (about 411,000 records):
<!--more-->
```console
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
```
- AReS went down when the `renew-letsencrypt` service stopped the `angular_nginx` container in the pre-update hook and failed to bring it back up
- I ran all system updates on the host and rebooted it and AReS came back up OK
## 2020-12-02
- Udana emailed me yesterday to ask why the CGSpace usage statistics were showing "No Data"
- I noticed a message in the Solr Admin UI that one of the statistics cores failed to load, but it is up and I can query it...
- Nevertheless, I restarted Tomcat a few times to see if all cores would come up without an error message, but had no success (despite that all cores ARE up and I can query them, _sigh_)
- I think I will move all the Solr yearly statistics back into the main statistics core
- Start testing export/import of yearly Solr statistics data into the main statistics core on DSpace Test, for example:
```
$ ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:*</query></delete>"
```
- I deployed Tomcat 7.0.107 on DSpace Test (CGSpace is still Tomcat 7.0.104)
- I finished migrating all the statistics from the yearly shards back to the main core
## 2020-12-05
- I deleted all the yearly statistics shards and restarted Tomcat on DSpace Test (linode26)
## 2020-12-06
- Looking into the statistics on DSpace Test after I migrated them back to the main core
- All stats are working as expected... indexing time for the DSpace Statistics API is the same... and I don't even see a difference in the JVM or memory stats in Munin other than a minor jump last week when I was processing them
- I will migrate them on CGSpace too I think
- First I will start with the statistics-2010 and statistics-2015 cores because they were the ones that were failing to load recently (despite actually being available in Solr WTF)
![Error message in Solr admin UI about the statistics-2010 core failing to load](/cgspace-notes/2020/12/solr-statistics-2010-failed.png)
- First the 2010 core:
```console
$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:*</query></delete>"
```
- Judging by the DSpace logs all these cores had a problem starting up in the last month:
```console
# grep -rsI "Unable to create core" [dspace]/log/dspace.log.2020-* | grep -o -E "statistics-[0-9]+" | sort | uniq -c
24 statistics-2010
24 statistics-2015
18 statistics-2016
6 statistics-2018
```
- The message is always this:
```
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error CREATEing SolrCore 'statistics-2016': Unable to create core [statistics-2016] Caused by: Lock obtain timed out: NativeFSLock@/[dspace]/solr/statistics-2016/data/index/write.lock
```
- I will migrate all these cores and see if it makes a difference, then probably end up migrating all of them
- I removed the statistics-2010, statistics-2015, statistics-2016, and statistics-2018 cores and restarted Tomcat and _all the statistics cores came up OK and the CUA statistics are OK_!
## 2020-12-07
- Run `dspace cleanup -v` on CGSpace to clean up deleted bitstreams
- Atmire sent a [pull request](https://github.com/ilri/DSpace/pull/457) to address the duplicate owningComm and owningColl
- Built and deployed it on DSpace Test but I am not sure how to run it yet
- I sent feedback to Atmire on their tracker: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839
- Abenet and Tezira are having issues with committing to the archive in their workflow
- I looked at the server and indeed the locks and transactions are back up:
![PostgreSQL Transactions day](/cgspace-notes/2020/12/postgres_transactions_ALL-day.png)
![PostgreSQL Locks day](/cgspace-notes/2020/12/postgres_locks_ALL-day.png)
![PostgreSQL Locks day](/cgspace-notes/2020/12/postgres_querylength_ALL-day.png)
![PostgreSQL Connections day](/cgspace-notes/2020/12/postgres_connections_ALL-day.png)
- There are apparently 1,700 locks right now:
```console
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1739
```
## 2020-12-08
- Atmire sent some instructions for using the DeduplicateValuesProcessor
- I modified `atmire-cua-update.xml` as they instructed, but I get a million errors like this when I run AtomicStatisticsUpdateCLI with that configuration:
```
Record uid: 64387815-d9a7-4605-8024-1c0a5c7520e0 couldn't be processed
com.atmire.statistics.util.update.atomic.ProcessingException: something went wrong while processing record uid: 64387815-d9a7-4605-8024-1c0a5c7520e0, an error occured in the com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor
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.UnsupportedOperationException
at org.apache.solr.common.SolrDocument$1.entrySet(SolrDocument.java:256)
at java.util.HashMap.putMapEntries(HashMap.java:512)
at java.util.HashMap.<init>(HashMap.java:490)
at com.atmire.statistics.util.update.atomic.record.Record.getFieldValuesMap(SourceFile:86)
at com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor.process(SourceFile:38)
at com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor.visit(SourceFile:34)
at com.atmire.statistics.util.update.atomic.record.UsageRecord.accept(SourceFile:23)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.applyProcessors(SourceFile:301)
... 10 more
```
- I sent some feedback to Atmire
- They responded with an updated CUA (6.x-4.1.10-ilri-RC7) that has a fix for the duplicates processor _and_ a possible fix for the database locking issues (a bug in CUASolrLoggerServiceImpl that causes an infinite loop and a Tomcat timeout)
- I deployed the changes on DSpace Test and CGSpace, hopefully it will fix both issues!
- In other news, after I restarted Tomcat on CGSpace the statistics-2013 core didn't come back up properly, so I exported it and imported it into the main statistics core like I did for the others a few days ago
- Sync DSpace Test with CGSpace's Solr, PostgreSQL database, and assetstore...
## 2020-12-09
- I was running the AtomicStatisticsUpdateCLI to remove duplicates on DSpace Test but it failed near the end of the statistics core (after 20 hours or so) with a memory error:
```
Successfully finished updating Solr Storage Reports | Wed Dec 09 15:25:11 CET 2020
Run 1 —  67% — 10,000/14,935 docs — 6m 6s — 6m 6s
Exception: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
at org.noggit.CharArr.toString(CharArr.java:164)
```
- I increased the JVM heap to 2048m and tried again, but it failed with a memory error again...
- I increased the JVM heap to 4096m and tried again, but it failed with another error:
```
Successfully finished updating Solr Storage Reports | Wed Dec 09 15:53:40 CET 2020
Exception: parsing error
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: parsing error
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:530)
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.QueryRequest.process(QueryRequest.java:91)
at org.apache.solr.client.solrj.SolrServer.query(SolrServer.java:301)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.getNextSetOfSolrDocuments(SourceFile:392)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:157)
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: org.apache.solr.common.SolrException: parsing error
at org.apache.solr.client.solrj.impl.BinaryResponseParser.processResponse(BinaryResponseParser.java:45)
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:528)
... 14 more
Caused by: org.apache.http.TruncatedChunkException: Truncated chunk ( expected size: 8192; actual size: 2843)
at org.apache.http.impl.io.ChunkedInputStream.read(ChunkedInputStream.java:200)
at org.apache.http.conn.EofSensorInputStream.read(EofSensorInputStream.java:137)
at org.apache.solr.common.util.FastInputStream.readWrappedStream(FastInputStream.java:80)
at org.apache.solr.common.util.FastInputStream.refill(FastInputStream.java:89)
at org.apache.solr.common.util.FastInputStream.read(FastInputStream.java:125)
at org.apache.solr.common.util.FastInputStream.readFully(FastInputStream.java:152)
...
```
## 2020-12-10
- The statistics-2019 core finished processing the duplicate removal so I started the statistics-2017 core
- Peter asked me to add ONE HEALTH to ILRI subjects on CGSpace
- A few items that got "lost" after approval during the database issues earlier this week seem to have gone back into their workflows
- Abenet approved them again and they got new handles, phew
- Abenet was having an issue with the date filter on AReS and it turns out that it's the same `.keyword` issue I had noticed before that causes the filter to stop working
- I fixed the filter to use the correct field name and filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/63
- I checked the Solr statistics on DSpace Test to see if the Atmire duplicates remover was working, but now I see a comical amount of duplicates...
![Solr stats with dozens of duplicates](/cgspace-notes/2020/12/solr-stats-duplicates.png)
- I sent feedback about this to Atmire
- I will re-sync the Solr stats from CGSpace so we can try again...
- In other news, it has been a few days since we deployed the fix for the database locking issue and things seem much better now:
![PostgreSQL connections all week](/cgspace-notes/2020/12/postgres_connections_ALL-week.png)
![PostgreSQL locks all week](/cgspace-notes/2020/12/postgres_locks_ALL-week.png)
## 2020-12-13
- I tried to harvest a few times on OpenRXV in the last few days and every time it appends all the new records to the items index instead of overwriting it:
![OpenRXV duplicates](/cgspace-notes/2020/12/openrxv-duplicates.png)
- I can see it in the `openrxv-items-final` index:
```console
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*' | json_pp
{
"_shards" : {
"failed" : 0,
"skipped" : 0,
"successful" : 1,
"total" : 1
},
"count" : 299922
}
```
- I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/64
- For now I will try to delete the index and start a re-harvest in the Admin UI:
```
$ curl -XDELETE http://localhost:9200/openrxv-items-final
{"acknowledged":true}%
```
- Moayad said he's working on the harvesting so I stopped it for now to re-deploy his latest changes
- I updated Tomcat to version 7.0.107 on CGSpace (linode18), ran all updates, and restarted the server
- I deleted both items indexes and restarted the harvesting:
```
$ curl -XDELETE http://localhost:9200/openrxv-items-final
$ curl -XDELETE http://localhost:9200/openrxv-items-temp
```
<!-- vim: set sw=2 ts=2: -->
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