--- 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): ```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 "*:*" ``` - 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 "*:*" ``` - 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.(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. (/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 real 265m11.224s user 171m29.141s sys 2m41.097s ``` - 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 - Yesterday Atmire responded about the owningComm and owningColl duplicates in Solr saying they didn't see any anymore... - Indeed I spent a few minutes looking randomly and I didn't find any either... - I did, however, see lots of duplicates in countryCode_search, countryCode_ngram, ip_search, ip_ngram, userAgent_search, userAgent_ngram, referrer_search, referrer_ngram fields - I sent feedback to them - On the database locking front we haven't had issues in over a week and the Munin graphs look normal: ![PostgreSQL connections all week](/cgspace-notes/2020/12/postgres_connections_ALL-week2.png) ![PostgreSQL locks all week](/cgspace-notes/2020/12/postgres_locks_ALL-week2.png) - After the Discovery re-indexing finished on CGSpace I prepared to start re-harvesting AReS by making sure the `openrxv-items-temp` index was empty and that the backup index I made yesterday was still there: ```console $ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty' { "acknowledged" : true } $ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty' { "count" : 0, "_shards" : { "total" : 1, "successful" : 1, "skipped" : 0, "failed" : 0 } } $ curl -s 'http://localhost:9200/openrxv-items-2020-12-14/_count?q=*&pretty' { "count" : 99992, "_shards" : { "total" : 1, "successful" : 1, "skipped" : 0, "failed" : 0 } } ``` ## 2020-12-16 - The harvesting on AReS finished last night so this morning I manually cloned the `openrxv-items-temp` index to `openrxv-items` - First check the number of items in the temp index, then set it to read only, then delete the items index, then delete the temp index: ```console $ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty' { "count" : 100046, "_shards" : { "total" : 1, "successful" : 1, "skipped" : 0, "failed" : 0 } } $ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}' $ curl -XDELETE 'http://localhost:9200/openrxv-items?pretty' $ curl -s -X POST "http://localhost:9200/openrxv-items-temp/_clone/openrxv-items?pretty" $ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty' { "count" : 100046, "_shards" : { "total" : 1, "successful" : 1, "skipped" : 0, "failed" : 0 } } $ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}' $ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty' ``` - Interestingly [the item](https://hdl.handle.net/10568/110447) that we noticed was duplicated now only appears once - The [missing item](https://hdl.handle.net/10568/110133) is still missing - Jane Poole noticed that the "previous page" and "next page" buttons are not working on AReS - I filed a bug on GitHub: https://github.com/ilri/OpenRXV/issues/65 - Generate a list of submitters and approvers active in the last months using the Provenance field on CGSpace: ```console $ psql -h localhost -U postgres dspace -c "SELECT text_value FROM metadatavalue WHERE metadata_field_id=28 AND text_value ~ '^.*on 2020-(06|07|08|09|10|11|12)-*'" > /tmp/provenance.txt $ grep -o -E 'by .*)' /tmp/provenance.txt | grep -v -E "( on |checksum)" | sed -e 's/by //' -e 's/ (/,/' -e 's/)//' | sort | uniq > /tmp/recent-submitters-approvers.csv ``` - Peter wanted it to send some mail to the users... ## 2020-12-17 - I see some errors from CUA in our Tomcat logs: ```console Thu Dec 17 07:35:27 CET 2020 | Query:containerItem:b049326a-0e76-45a8-ac0c-d8ec043a50c6 Error while updating java.lang.UnsupportedOperationException: Multiple update components target the same field:solr_update_time_stamp at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1155) at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:241) at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1140) at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1129) ... ``` - I sent the full stack to Atmire to investigate - I know we've had thisi "Multiple update components target the same field" error in the past with DSpace 5.x and Atmire said it was harmless, but would nevertheless be fixed in a future update - I was trying to export the ILRI community on CGSpace so I could update one of the ILRI author's names, but it throws an error... ```console $ dspace metadata-export -i 10568/1 -f /tmp/2020-12-17-ILRI.csv Loading @mire database changes for module MQM Changes have been processed Exporting community 'International Livestock Research Institute (ILRI)' (10568/1) Exception: null java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:212) at com.google.common.collect.Iterators.concat(Iterators.java:464) at org.dspace.app.bulkedit.MetadataExport.addItemsToResult(MetadataExport.java:136) at org.dspace.app.bulkedit.MetadataExport.buildFromCommunity(MetadataExport.java:125) at org.dspace.app.bulkedit.MetadataExport.(MetadataExport.java:77) at org.dspace.app.bulkedit.MetadataExport.main(MetadataExport.java:282) 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) ``` - I did it via CSV with `fix-metadata-values.py` instead: ```console $ cat 2020-12-17-update-ILRI-author.csv dc.contributor.author,correct "Padmakumar, V.P.","Varijakshapanicker, Padmakumar" $ ./fix-metadata-values.py -i 2020-12-17-update-ILRI-author.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t 'correct' -m 3 - Abenet needed a list of all 2020 outputs from the Livestock CRP that were Limited Access - I exported the community from CGSpace and used `csvcut` and `csvgrep` to get a list: ``` $ csvcut -c 'dc.identifier.citation[en_US],dc.identifier.uri,dc.identifier.uri[],dc.identifier.uri[en_US],dc.date.issued,dc.date.issued[],dc.date.issued[en_US],cg.identifier.status[en_US]' ~/Downloads/10568-80099.csv | csvgrep -c 'cg.identifier.status[en_US]' -m 'Limited Access' | csvgrep -c 'dc.date.issued' -m 2020 -c 'dc.date.issued[]' -m 2020 -c 'dc.date.issued[en_US]' -m 2020 > /tmp/limited-2020.csv ``` ## 2020-12-18 - I added support for indexing community views and downloads to [dspace-statistics-api](https://github.com/ilri/dspace-statistics-api) - I still have to add the API endpoints to make the stats available - Also, I played a little bit with Swagger via [falcon-swagger-ui](https://github.com/rdidyk/falcon-swagger-ui) and I think I can get that working for better API documentation / testing - Atmire sent some feedback on the DeduplicateValuesProcessor - They confirm that it should process _all_ duplicates, not just those in `owningComm` and `owningColl` - They asked me to try it again on DSpace Test now that I've resync'd the Solr statistics cores from production - I started processing the statistics core on DSpace Test ## 2020-12-20 - The DeduplicateValuesProcessor has been running on DSpace Test since two days ago and it almost completed its second twelve-hour run, but crashed near the end: ```console ... Run 1 — 100% — 8,230,000/8,239,228 docs — 39s — 9h 8m 31s Exception: Java heap space java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOfRange(Arrays.java:3664) at java.lang.String.(String.java:207) at org.noggit.CharArr.toString(CharArr.java:164) at org.apache.solr.common.util.JavaBinCodec.readStr(JavaBinCodec.java:599) at org.apache.solr.common.util.JavaBinCodec.readVal(JavaBinCodec.java:180) at org.apache.solr.common.util.JavaBinCodec.readArray(JavaBinCodec.java:492) at org.apache.solr.common.util.JavaBinCodec.readVal(JavaBinCodec.java:186) at org.apache.solr.common.util.JavaBinCodec.readSolrDocument(JavaBinCodec.java:360) at org.apache.solr.common.util.JavaBinCodec.readVal(JavaBinCodec.java:219) at org.apache.solr.common.util.JavaBinCodec.readArray(JavaBinCodec.java:492) at org.apache.solr.common.util.JavaBinCodec.readVal(JavaBinCodec.java:186) at org.apache.solr.common.util.JavaBinCodec.readSolrDocumentList(JavaBinCodec.java:374) at org.apache.solr.common.util.JavaBinCodec.readVal(JavaBinCodec.java:221) at org.apache.solr.common.util.JavaBinCodec.readOrderedMap(JavaBinCodec.java:125) at org.apache.solr.common.util.JavaBinCodec.readVal(JavaBinCodec.java:188) at org.apache.solr.common.util.JavaBinCodec.unmarshal(JavaBinCodec.java:116) at org.apache.solr.client.solrj.impl.BinaryResponseParser.processResponse(BinaryResponseParser.java:43) at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:528) 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) ``` - That was with a JVM heap of 512m - I looked in Solr and found dozens of duplicates of each field again... - I sent [feedback to Atmire](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839) - I finished the technical work on adding community and collection support to the DSpace Statistics API - I still need to update ~~the tests~~ as well as the documentation - I started a harvesting of AReS ## 2020-12-21 - The AReS harvest finished this morning and I moved the Elasticsearch index manually - First, check the number of records in the temp index to make sure it seems complete and not with double data: ```console $ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty' { "count" : 100135, "_shards" : { "total" : 1, "successful" : 1, "skipped" : 0, "failed" : 0 } } ``` - Then delete the old backup and clone the current items index as a backup: ```console $ curl -XDELETE 'http://localhost:9200/openrxv-items-2020-12-14?pretty' $ curl -X PUT "localhost:9200/openrxv-items/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}' $ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2020-12-21 ``` - Then delete the current items index and clone it from temp: ```console $ curl -XDELETE 'http://localhost:9200/openrxv-items?pretty' $ 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 $ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}' ``` ## 2020-12-22 - I finished getting the Swagger UI integrated into the dspace-statistics-api - I can't figure out how to get it to work on the server without hard-coding all the paths - Falcon is smart about its own routes, so I can retrieve the `openapi.json` file OK, but the paths in the OpenAPI schema are relative to the base URL, which is `dspacetest.cgiar.org` - Abenet told me about a bug with shared links and strange values in the top counters - I took a video reproducing the issue and filed a bug on the GitHub: https://github.com/ilri/OpenRXV/issues/66 ## 2020-12-23 - Finalize Swagger UI support in the dspace-statistics-api - I had to do some last minute changes to get it to work in both production and local development environments ## 2020-12-27 - More finishing touches on paging and versioning of the dspace-statistics-api - I tagged v1.4.0 and released it on GitHub: https://github.com/ilri/dspace-statistics-api/releases/tag/v1.4.0 - I deployed it on DSpace Test and CGSpace ## 2020-12-28 - Peter noticed that the Atmire CUA stats on CGSpace weren't working - I looked in Solr Admin UI and saw that the statistics-2012 core failed to load: ``` statistics-2012: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher ``` - I exported the 2012 stats from the year core and imported them to the main statistics core with solr-import-export-json: ```console $ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics-2012 -a export -o statistics-2012.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-2012/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "*:*" ``` - I decided to do the same for the remaining 2011, 2014, 2017, and 2019 cores... ## 2020-12-29 - Start a fresh re-index on AReS, since it's been over a week since the last time - Before then I cleared the old `openrxv-items-temp` index and made a backup of the current `openrxv-items` index: ```console $ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty' { "count" : 100135, "_shards" : { "total" : 1, "successful" : 1, "skipped" : 0, "failed" : 0 } } $ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty' $ curl -X PUT "localhost:9200/openrxv-items/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}' $ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2020-12-29 $ curl -X PUT "localhost:9200/openrxv-items/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}' ``` ## 2020-12-30 - The indexing on AReS finished so I cloned the `openrxv-items-temp` index to `openrxv-items` and deleted the backup index: ```console $ curl -XDELETE 'http://localhost:9200/openrxv-items?pretty' $ 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 $ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}' $ curl -XDELETE 'http://localhost:9200/openrxv-items-temp?pretty' $ curl -XDELETE 'http://localhost:9200/openrxv-items-2020-12-29?pretty' ```