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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
```
- Peter asked me for a list of all submitters and approvers that were active recently on CGSpace
- I can probably extract that from the `dc.description.provenance` field, for example any that contains a 2020 date:
```console
localhost/dspace63= > SELECT * FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-[0-9]{2}-*';
```
## 2020-12-14
- The re-harvesting finished last night on AReS but there are no records in the `openrxv-items-final` index
- Strangely, there are 99,000 items in the temp index:
```console
$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*' | json_pp
{
"count" : 99992,
"_shards" : {
"skipped" : 0,
"total" : 1,
"failed" : 0,
"successful" : 1
}
}
```
- I'm going to try to [clone](https://www.elastic.co/guide/en/elasticsearch/reference/master/indices-clone-index.html) the temp index to the final one...
- First, set the `openrxv-items-temp` index to block writes (read only) and then clone it to `openrxv-items-final`:
```console
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final"}
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
```
- Now I see that the `openrxv-items-final` index has items, but there are still none in AReS Explorer UI!
```console
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
{
"count" : 99992,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
```
- The api logs show this from last night after the harvesting:
```console
[Nest] 92 - 12/13/2020, 1:58:52 PM [HarvesterService] Starting Harvest
[Nest] 92 - 12/13/2020, 10:50:20 PM [FetchConsumer] OnGlobalQueueDrained
[Nest] 92 - 12/13/2020, 11:00:20 PM [PluginsConsumer] OnGlobalQueueDrained
[Nest] 92 - 12/13/2020, 11:00:20 PM [HarvesterService] reindex function is called
(node:92) UnhandledPromiseRejectionWarning: ResponseError: index_not_found_exception
at IncomingMessage.<anonymous> (/backend/node_modules/@elastic/elasticsearch/lib/Transport.js:232:25)
at IncomingMessage.emit (events.js:326:22)
at endReadableNT (_stream_readable.js:1223:12)
at processTicksAndRejections (internal/process/task_queues.js:84:21)
```
- But I'm not sure why the frontend doesn't show any data despite there being documents in the index...
- I talked to Moayad and he reminded me that OpenRXV uses an alias to point to temp and final indexes, but the UI actually uses the `openrxv-items` index
- I cloned the `openrxv-items-final` index to `openrxv-items` index and now I see items in the explorer UI
- The PDF report was broken and I looked in the API logs and saw this:
```console
(node:94) UnhandledPromiseRejectionWarning: Error: Error: Could not find soffice binary
at ExportService.downloadFile (/backend/dist/export/services/export/export.service.js:51:19)
at processTicksAndRejections (internal/process/task_queues.js:97:5)
```
- I installed `unoconv` in the backend api container and now it works... but I wonder why this changed...
- Skype with Abenet and Peter to discuss AReS that will be shown to ILRI scientists this week
- Peter noticed that [this item](https://hdl.handle.net/10568/110133) from the [ILRI policy and research briefs](https://cgspace.cgiar.org/handle/10568/24450) collection is missing in AReS, despite it being added one month ago in CGSpace and me harvesting on AReS last night
- The item appears fine in the REST API when I check the items in that collection
- Peter also noticed that [this item](https://hdl.handle.net/10568/110447) appears twice in AReS
- The item is _not_ duplicated on CGSpace or in the REST API
- We noticed that there are 136 items in the ILRI policy and research briefs collection according to AReS, yet on CGSpace there are only 132
- This is confirmed in the REST API (using [query-json](https://github.com/davesnx/query-json)):
```
$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&limit=100&offset=0' | json_pp > /tmp/policy1.json
$ http --print b 'https://cgspace.cgiar.org/rest/collections/defee001-8cc8-4a6c-8ac8-21bb5adab2db?expand=all&limit=100&offset=100' | json_pp > /tmp/policy2.json
$ query-json '.items | length' /tmp/policy1.json
100
$ query-json '.items | length' /tmp/policy2.json
32
```
- I realized that the issue of missing/duplicate items in AReS might be because of this [REST API bug that causes /items to return items in non-deterministic order](https://jira.lyrasis.org/browse/DS-3849)
- I decided to cherry-pick the following two patches from DSpace 6.4 into our `6_x-prod` (6.3) branch:
- High CPU usage when calling the collection_id/items REST endpoint
- Jira: https://jira.lyrasis.org/browse/DS-4342
- c2e6719fa763e291b81b2d61da2f8c758fe38ff3
- REST API items resource returns items in non-deterministic order
- Jira: https://jira.lyrasis.org/browse/DS-3849
- 2a2ea0cb5d03e6da9355a2eff12aad667e465433
- After deploying the REST API fixes I decided to harvest from AReS again to see if the missing and duplicate items get fixed
- I made a backup of the current `openrxv-items-temp` index just in case:
```console
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-2020-12-14
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
```
## 2020-12-15
- After the re-harvest last night there were 200,000 items in the `openrxv-items-temp` index again
- I cleared the core and started a re-harvest, but Peter sent me a bunch of author corrections for CGSpace so I decided to cancel it until after I apply them and re-index Discovery
- I checked the 1,534 fixes in Open Refine (had to fix a few UTF-8 errors, as always from Peter's CSVs) and then applied them using the `fix-metadata-values.py` script:
```console
$ ./fix-metadata-values.py -i /tmp/2020-10-28-fix-1534-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3
$ ./delete-metadata-values.py -i /tmp/2020-10-28-delete-2-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -m 3
```
- Since I was re-indexing Discovery anyways I decided to check for any uppercase AGROVOC and lowercase them:
```console
dspace=# BEGIN;
BEGIN
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
UPDATE 406
dspace=# COMMIT;
COMMIT
```
- I also updated the Font Awesome icon classes for version 5 syntax:
```console
dspace=# BEGIN;
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-rss','fas fa-rss', 'g') WHERE text_value LIKE '%fa fa-rss%';
UPDATE 74
dspace=# UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, 'fa fa-at','fas fa-at', 'g') WHERE text_value LIKE '%fa fa-at%';
UPDATE 74
dspace=# COMMIT;
```
- Then I started a full Discovery re-index:
```console
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m"
$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
```
- Udana sent a report that the WLE approver is experiencing the same issue Peter highlighted a few weeks ago: they are unable to save metadata edits in the workflow
<!-- vim: set sw=2 ts=2: -->
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