November, 2020

Sun Nov 01, 2020 in Notes

2020-11-01

Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
- So far we’ve spent at least fifty hours to process the statistics and statistics-2019 core… wow.

2020-11-02

Talk to Moayad and fix a few issues on OpenRXV:
- Incorrect views and downloads (caused by Elasticsearch’s default result set size of 10)
- Invalid share link
- Missing “https://” for Handles in the Simple Excel report (caused by using the handle instead of the uri)
- Sorting the list of items by views
I resumed the processing of the statistics-2018 Solr core after it spent 20 hours to get to 60%

2020-11-04

After 29 hours the statistics-2017 core finished processing so I started the statistics-2016 core on DSpace Test

2020-11-05

Peter sent me corrections and deletions for the author affiliations
- I quickly proofed them for UTF-8 issues in OpenRefine and csv-metadata-quality and then tested them locally and then applied them on CGSpace:

$ ./fix-metadata-values.py -i 2020-11-05-fix-862-affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t 'correct' -m 211
$ ./delete-metadata-values.py -i 2020-11-05-delete-29-affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211

Then I started a Discovery re-index on CGSpace:

$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b

real    92m24.993s
user    8m11.858s
sys     2m26.931s

2020-11-06

Restart the AtomicStatisticsUpdateCLI processing of the statistics-2016 core on DSpace Test after 20 hours…
- This phase finished after five hours so I started it on the statistics-2015 core

2020-11-07

Atmire responded about the issue with duplicate values in owningComm and containerCommunity etc
- I told them to please look into it and use some of our credits if need be
The statistics-2015 core finished after 20 hours so I started the statistics-2014 core

2020-11-08

Add “Data Paper” to types on CGSpace
Add “SCALING CLIMATE-SMART AGRICULTURE” to CCAFS subjects on CGSpace
Add “ANDEAN ROOTS AND TUBERS” to CIP subjects on CGSpace
Add CGIAR System subjects to Discovery sidebar facets on CGSpace
- Also add the System subject to item view on CGSpace
The statistics-2014 core finished processing after five hours, so I started processing the statistics-2013 core on DSpace Test
Since I was going to restart CGSpace and update the Discovery indexes anyways I decided to check for any straggling upper case AGROVOC entries and lower case them:

dspace=# BEGIN;
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE resource_type_id=2 AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
UPDATE 164
dspace=# COMMIT;

Run system updates on CGSpace (linode18) and reboot it
- I had to restart Tomcat once after the machine started up to get all Solr statistics cores to load properly
After about ten more hours the rest of the Solr statistics cores finished processing on DSpace Test and I started optimizing them in Solr admin UI

2020-11-10

I am noticing that CGSpace doesn’t have any statistics showing for years before 2020, but all cores are loaded successfully in Solr Admin UI… strange
- I restarted Tomcat and I see in Solr Admin UI that the statistics-2015 core failed to load
- Looking in the DSpace log I see:

2020-11-10 08:43:59,634 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:43:59,687 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2018
2020-11-10 08:43:59,707 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:44:00,004 WARN  org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,005 WARN  org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,005 WARN  org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,325 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2015

Seems that the core gets probed twice… perhaps a threading issue?
- The only thing I can think of is the acceptorThreadCount parameter in Tomcat’s server.xml, which has been set to 2 since 2018-01 (we started sharding the Solr statistics cores in 2019-01 and that’s when this problem arose)
- I will try reducing that to 1
- Wow, now it’s even worse:

2020-11-10 08:51:03,007 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2018
2020-11-10 08:51:03,008 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:51:03,137 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2018
2020-11-10 08:51:03,153 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:51:03,289 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2015
2020-11-10 08:51:03,289 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2010
2020-11-10 08:51:03,475 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2010
2020-11-10 08:51:03,475 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2016
2020-11-10 08:51:03,730 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2016
2020-11-10 08:51:03,731 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2017
2020-11-10 08:51:03,992 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2017
2020-11-10 08:51:03,992 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2011
2020-11-10 08:51:04,178 INFO  org.dspace.statistics.SolrLogger @ Created core with name: statistics-2011
2020-11-10 08:51:04,178 INFO  org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2012

Could it be because we have two Tomcat connectors?
- I restarted Tomcat a few more times before all cores loaded, and still there are no stats before 2020-01… hmmmmm
I added a lowercase formatter to OpenRXV so that we can lowercase AGROVOC subjects during harvesting

2020-11-11

Atmire responded with a quote for the work to fix the duplicate owningComm, etc in our Solr data
- I told them to proceed, as it’s within our budget of credits
- They will write a processor for DSpace 6 to remove the duplicates
I did some tests to add a usage statistics chart to the item views on DSpace Test
- It is inspired by Salem’s work on WorldFish’s repository, and it hits the dspace-statistics-api for the current item and displays a graph
- I got it working very easily for all-time statistics with Chart.js, but I think I will need to use Highcharts or something else because Chart.js is HTML5 canvas and doesn’t allow theming via CSS (so our Bootstrap brand colors for each theme won’t work)
  - Hmm, Highcharts is not licensed under and open source license so I will not use it
  - Perhaps I’ll use Chartist with the popover plugin…
- I think I’ll pursue this after the DSpace 6 upgrade…

2020-11-12

I was looking at Solr again trying to find a way to get community and collection stats by faceting on owningComm and owningColl and it seems to work actually
- The duplicated values in the multi-value fields don’t seem to affect the counts, as I had thought previously (though we should still get rid of them)
- One major difference between the raw numbers I was looking at and Atmire’s numbers is that Atmire’s code filters “Internal” IP addresses…
- Also, instead of doing isBot:false I think I should do -isBot:true because it’s not a given that all documents will have this field and have it false, but we can definitely exclude the ones that have it as true
First we get the total number of communities with stats (using calcdistinct):

facet=true&facet.field=owningComm&facet.mincount=1&facet.limit=1&facet.offset=0&stats=true&stats.field=owningComm&stats.calcdistinct=true&shards=http://localhost:8081/solr/statistics,http://localhost:8081/solr/statistics-2019,http://localhost:8081/solr/statistics-2018,http://localhost:8081/solr/statistics-2017,http://localhost:8081/solr/statistics-2016,http://localhost:8081/solr/statistics-2015,http://localhost:8081/solr/statistics-2014,http://localhost:8081/solr/statistics-2013,http://localhost:8081/solr/statistics-2012,http://localhost:8081/solr/statistics-2011,http://localhost:8081/solr/statistics-2010

Then get stats themselves, iterating 100 items at a time with limit and offset:

facet=true&facet.field=owningComm&facet.mincount=1&facet.limit=100&facet.offset=0&shards=http://localhost:8081/solr/statistics,http://localhost:8081/solr/statistics-2019,http://localhost:8081/solr/statistics-2018,http://localhost:8081/solr/statistics-2017,http://localhost:8081/solr/statistics-2016,http://localhost:8081/solr/statistics-2015,http://localhost:8081/solr/statistics-2014,http://localhost:8081/solr/statistics-2013,http://localhost:8081/solr/statistics-2012,http://localhost:8081/solr/statistics-2011,http://localhost:8081/solr/statistics-2010

I was surprised to see 10,000,000 docs with isBot:true when I was testing on DSpace Test…
- This has got to be a mistake of some kind, as I see 4 million in 2014 that are from dns:localhost., perhaps that’s when we didn’t have useProxies set up correctly?
- I don’t see the same thing on CGSpace… I wonder what happened?
- Perhaps they got re-tagged during the DSpace 6 upgrade, somehow during the Solr migration? Hmmmmm. Definitely have to be careful with isBot:true in the future and not automatically purge these!!!
I noticed 120,000+ hits from monit, FeedBurner, and Blackboard Safeassign in 2014, 2015, 2016, 2017, etc…
- I hadn’t seen monit before, but the others are already in DSpace’s spider agents lists for some time so probably only appear in older stats cores
- The issue with purging these using check-spider-hits.sh is that it can’t do case-insensitive regexes and some metacharacters like \s don’t work so I added case-sensitive patterns to a local agents file and purged them with the script

2020-11-15

Upgrade CGSpace to DSpace 6.3
- First build, update, and migrate the database:

$ dspace cleanup -v
$ git checkout origin/6_x-dev-atmire-modules
$ npm install -g yarn
$ chrt -b 0 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2,\!dspace-jspui clean package
$ sudo su - postgres
$ psql dspace -c 'CREATE EXTENSION pgcrypto;'
$ psql dspace -c "DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');"
$ exit
$ rm -rf /home/cgspace/config/spring
$ ant update
$ dspace database info
$ dspace database migrate
$ sudo systemctl start tomcat7

After starting Tomcat DSpace should start up OK and begin Discovery indexing, but I want to also upgrade from PostgreSQL 9.6 to 10
- I installed and configured PostgreSQL 10 using the Ansible playbooks, then migrated the database manually:

# systemctl stop tomcat7
# pg_ctlcluster 9.6 main stop
# tar -cvzpf var-lib-postgresql-9.6.tar.gz /var/lib/postgresql/9.6
# tar -cvzpf etc-postgresql-9.6.tar.gz /etc/postgresql/9.6
# pg_ctlcluster 10 main stop
# pg_dropcluster 10 main
# pg_upgradecluster 9.6 main
# pg_dropcluster 9.6 main
# systemctl start postgresql
# dpkg -l | grep postgresql | grep 9.6 | awk '{print $2}' | xargs dpkg -r

Then I ran all system updates and rebooted the server…
After the server came back up I re-ran the Ansible playbook to make sure all configs and services were updated
I disabled the dspace-statistsics-api for now because it won’t work until I migrate all the Solr statistics anyways
Start a full Discovery re-indexing:

$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b

real    211m30.726s
user    134m40.124s
sys     2m17.979s

Towards the end of the indexing there were a few dozen of these messages:

2020-11-15 13:23:21,685 INFO  com.atmire.dspace.discovery.service.AtmireSolrService @ Removed Item: null from Index

I updated all the Ansible infrastructure and DSpace branches to be the DSpace 6 ones
I will wait until the Discovery indexing is finished to start doing the Solr statistics migration
I tested the email functionality and it seems to need more configuration:

$ dspace test-email

About to send test email:
 - To: blah@cgiar.org
 - Subject: DSpace test email
 - Server: smtp.office365.com

Error sending email:
 - Error: com.sun.mail.smtp.SMTPSendFailedException: 451 5.7.3 STARTTLS is required to send mail [AM4PR0701CA0003.eurprd07.prod.outlook.com]

I copied the mail.extraproperties = mail.smtp.starttls.enable=true setting from the old DSpace 5 dspace.cfg and now the emails are working
After the Discovery indexing finished I started processing the Solr stats one core and 2.5 million records at a time:

$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics

After about 6,000,000 records I got the same error that I’ve gotten every time I test this migration process:

Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
        at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
        at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
        at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
        at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
        at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
        at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
        at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
        at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)