cgspace-notes/content/posts/2020-03.md

---
title: "March, 2020"
date: 2020-03-02T12:31:30+02:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2020-03-02

- Update [dspace-statistics-api](https://github.com/ilri/dspace-statistics-api) for DSpace 6+ UUIDs
  - Tag version 1.2.0 on GitHub
- Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased [SolrUpgradePre6xStatistics.java](https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059)
  - You need to download this into the DSpace 6.x source and compile it

<!--more-->

```
$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x
```

## 2020-03-03

- Skype with Peter and Abenet to discuss the CG Core survey
  - We also discussed some other CGSpace issues

## 2020-03-04

- Abenet asked me to add some new ILRI subjects to CGSpace
  - I [updated the input-forms.xml](https://github.com/ilri/DSpace/commit/b51a242e773bd8658d3cab4ac883975708b00386) in our `5_x-prod` branch on GitHub
  - Abenet said we are changing `HEALTH` to `HUMAN HEALTH` so I need to fix those using my `fix-metadata-values.py` script:

```
$ ./fix-metadata-values.py -i 2020-03-04-fix-1-ilri-subject.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.ilri -m 203 -t correct -d
```

- But I have not run it on CGSpace yet because we want to ask Peter if he is sure about it...
- Send a message to Macaroni Bros to ask them about their Drupal module and its readiness for DSpace 6 UUIDs

## 2020-03-05

- I found a very [interesting comment on the Solr 8.1 guide](https://lucene.apache.org/solr/guide/8_1/solr-system-requirements.html#lucene-solr-prior-to-7-0) about Java compatibility:

> Lucene/Solr 7.0 was the first version that successfully passed our tests using Java 9 and higher. You should avoid Java 9 or later for Lucene/Solr 6.x or earlier.

## 2020-03-08

- I want to try to consolidate our yearly Solr statistics cores back into one `statistics` core using the solr-import-export-json tool
- I will try it on DSpace test, doing one year at a time:

```
$ ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o /tmp/statistics-2010.json -k uid
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/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>time:2010*</query></delete>"
$ ./run.sh -s http://localhost:8081/solr/statistics-2011 -a export -o /tmp/statistics-2011.json -k uid
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2011.json -k uid
$ curl -s "http://localhost:8081/solr/statistics-2011/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2011*</query></delete>"
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2012.json -k uid
$ curl -s 'http://localhost:8081/solr/statistics/select?q=time:2012*&rows=0&wt=json&indent=true' | grep numFound
  "response":{"numFound":3761989,"start":0,"docs":[]
$ curl -s 'http://localhost:8081/solr/statistics-2012/select?q=time:2012*&rows=0&wt=json&indent=true' | grep numFound
  "response":{"numFound":3761989,"start":0,"docs":[]
$ curl -s "http://localhost:8081/solr/statistics-2012/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2012*</query></delete>"
```

- I will do this for as many cores as I can (disk space limited) and then monitor the effect on the system and JVM memory usage
  - Exporting half years might work, using a filter query with months as a regular expression:

```
$ ./run.sh -s http://localhost:8081/solr/statistics-2014 -a export -o /tmp/statistics-2014-1.json -k uid -f 'time:/2014-0[1-6].*/'
```

- Upgrade PostgreSQL from 9.6 to 10 on DSpace Test (linode19)
  - I've been running it for one month in my local environment, and others have reported on the dspace-tech mailing list that they are using 10 and 11

```
# apt install postgresql-10 postgresql-contrib-10
# 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
# dpkg -l | grep postgresql | grep 9.6 | awk '{print $2}' | xargs dpkg -r
```

## 2020-03-09

- Peter noticed that the Solr stats were not showing anything before 2020
  - I had to restart Tomcat three times before all cores loaded properly...

## 2020-03-10

- Fix some logic issues in the nginx config
  - Use generic blocking of `[Bb]ot` and `[Cc]rawl` and `[Ss]pider` in the "badbots" rate limiting logic instead of trying to list them all one by one (bots should not be trying to index dynamic pages *no matter what* so we punish hard here)
  - We were not properly forwarding the remote IP address to Tomcat in all nginx location blocks, which led some locations to log a hit from 127.0.0.1 (because we need to explicitly add the global proxy params when setting other headers in location blocks)
  - Unfortunately this affected the REST API and there are a few hundred thousand requests from this user agent:

```
Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 (.NET CLR 3.5.30729)
```

- It seems to only be a problem in the last week:

```
# zgrep -c 64.225.40.66 /var/log/nginx/rest.log.{1..9}
/var/log/nginx/rest.log.1:0
/var/log/nginx/rest.log.2:0
/var/log/nginx/rest.log.3:0
/var/log/nginx/rest.log.4:3625
/var/log/nginx/rest.log.5:27458
/var/log/nginx/rest.log.6:0
/var/log/nginx/rest.log.7:0
/var/log/nginx/rest.log.8:0
/var/log/nginx/rest.log.9:0
```

- In Solr the IP is 127.0.0.1, but in the nginx logs I can luckily see the real IP (64.225.40.66), which is on Digital Ocean
- I will purge them from Solr statistics:

```
$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>userAgent:"Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 (.NET CLR 3.5.30729)"</query></delete>'
```

- Another user agent that seems to be a bot is:

```
Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)
```

- In Solr the IP is 127.0.0.1 because of the misconfiguration, but in nginx's logs I see it belongs to three IPs on Online.net in France:

```
# zcat /var/log/nginx/access.log.*.gz /var/log/nginx/rest.log.*.gz | grep 'Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)' | awk '{print $1}' | sort | uniq -c
  63090 163.172.68.99
 183428 163.172.70.248
 147608 163.172.71.24
```
- It is making 10,000 to 40,000 requests to XMLUI per day...

```
# zgrep -c 'Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)' /var/log/nginx/access.log.{1..9}
/var/log/nginx/access.log.30.gz:18687
/var/log/nginx/access.log.31.gz:28936
/var/log/nginx/access.log.32.gz:36402
/var/log/nginx/access.log.33.gz:38886
/var/log/nginx/access.log.34.gz:30607
/var/log/nginx/access.log.35.gz:19040
/var/log/nginx/access.log.36.gz:10780
/var/log/nginx/access.log.37.gz:5808
/var/log/nginx/access.log.38.gz:3100
/var/log/nginx/access.log.39.gz:1485
/var/log/nginx/access.log.3.gz:2898
/var/log/nginx/access.log.40.gz:373
/var/log/nginx/access.log.41.gz:3909
/var/log/nginx/access.log.42.gz:4729
/var/log/nginx/access.log.43.gz:3906
```

- I will purge those hits too!

```
$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>userAgent:"Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)"</query></delete>'
```

- Shit, and something happened and a few thousand hits from user agents with "Bot" in their user agent got through
  - I need to re-run the `check-bot-hits.sh` script with the standard COUNTER-Robots list again, but add my own versions of a few because the script/Solr doesn't support case-insensitive regular expressions:

```
$ ./check-spider-hits.sh -f /tmp/bots -d -p
(DEBUG) Using spiders pattern file: /tmp/bots
(DEBUG) Checking for hits from spider: Citoid
Purging 11 hits from Citoid in statistics
(DEBUG) Checking for hits from spider: ecointernet
Purging 375 hits from ecointernet in statistics
(DEBUG) Checking for hits from spider: ^Pattern\/[0-9]
Purging 1 hits from ^Pattern\/[0-9] in statistics
(DEBUG) Checking for hits from spider: sqlmap
(DEBUG) Checking for hits from spider: Typhoeus
Purging 6 hits from Typhoeus in statistics
(DEBUG) Checking for hits from spider: 7siters
(DEBUG) Checking for hits from spider: Apache-HttpClient
Purging 3178 hits from Apache-HttpClient in statistics

Total number of bot hits purged: 3571

$ ./check-spider-hits.sh -f /tmp/bots -d -p
(DEBUG) Using spiders pattern file: /tmp/bots
(DEBUG) Checking for hits from spider: [Bb]ot
Purging 8317 hits from [Bb]ot in statistics
(DEBUG) Checking for hits from spider: [Cc]rawl
Purging 1314 hits from [Cc]rawl in statistics
(DEBUG) Checking for hits from spider: [Ss]pider
Purging 62 hits from [Ss]pider in statistics
(DEBUG) Checking for hits from spider: Citoid
(DEBUG) Checking for hits from spider: ecointernet
(DEBUG) Checking for hits from spider: ^Pattern\/[0-9]
(DEBUG) Checking for hits from spider: sqlmap
(DEBUG) Checking for hits from spider: Typhoeus
(DEBUG) Checking for hits from spider: 7siters
(DEBUG) Checking for hits from spider: Apache-HttpClient
```

## 2020-03-11

- Ask Michael Victor for permission to create a new Linode server for DSpace Test

## 2020-3-12

- I'm working on the 170 IITA records on [DSpace Test](https://dspacetest.cgiar.org/handle/10568/106567) from January finally
  - It's been two months since I last looked and I want to do a thorough check to make sure Bosede didn't introduce any new issues, but I want to consolidate all the text languages for these records so it's easier to check them in OpenRefine
  - First I got a list of IDs from `csvcut` and then I updated the text languages for only those records:

```
dspace=# SELECT DISTINCT text_lang, COUNT(*) FROM metadatavalue WHERE resource_type_id=2 AND resource_id in (111295,111294,111293,111292,111291,111290,111288,111286,111285,111284,111283,111282,111281,111280,111279,111278,111277,111276,111275,111274,111273,111272,111271,111270,111269,111268,111267,111266,111265,111264,111263,111262,111261,111260,111259,111258,111257,111256,111255,111254,111253,111252,111251,111250,111249,111248,111247,111246,111245,111244,111243,111242,111241,111240,111238,111237,111236,111235,111234,111233,111232,111231,111230,111229,111228,111227,111226,111225,111224,111223,111222,111221,111220,111219,111218,111217,111216,111215,111214,111213,111212,111211,111209,111208,111207,111206,111205,111204,111203,111202,111201,111200,111199,111198,111197,111196,111195,111194,111193,111192,111191,111190,111189,111188,111187,111186,111185,111184,111183,111182,111181,111180,111179,111178,111177,111176,111175,111174,111173,111172,111171,111170,111169,111168,111299,111298,111297,111296,111167,111166,111165,111164,111163,111162,111161,111160,111159,111158,111157,111156,111155,111154,111153,111152,111151,111150,111149,111148,111147,111146,111145,111144,111143,111142,111141,111140,111139,111138,111137,111136,111135,111134,111133,111132,111131,111129,111128,111127,111126,111125) GROUP BY text_lang ORDER BY count;
```

- Then I exported the metadata from DSpace Test and imported it into OpenRefine
  - I corrected one invalid AGROVOC subject using my `csv-metadata-quality` script
- I exported a new list of affiliations from the database, added line numbers with `csvcut`, and then validated them in OpenRefine using `reconcile-csv`:


```
dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2020-03-12-affiliations.csv WITH CSV HEADER;`
dspace=# \q
$ csvcut -l -c 0 /tmp/2020-03-12-affiliations.csv | sed -e 's/^line_number/id/' -e 's/text_value/name/' > /tmp/affiliations.csv
$ lein run /tmp/affiliations.csv name id
```

- I always forget how to copy the reconciled values in OpenRefine, but you need to make a new column and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)`
- I mapped all 170 items to their appropriate collections based on type and uploaded them to CGSpace

## 2020-03-16

- I'm looking at the CPU usage of CGSpace (linode18) over the past year and I see we *rarely* even go over two CPUs on average sustained usage:

![linode18 CPU usage year](/cgspace-notes/2020/03/cgspace-cpu-year.png)

- Also clearly visible is the effect of CPU steal in 2019-03

![linode18 RAM usage year](/cgspace-notes/2020/03/cgspace-memory-year.png)

![linode18 JVM heap usage year](/cgspace-notes/2020/03/cgspace-heap-year.png)

- At max we have committed 10GB of RAM, the rest is used opportunistically by the filesystem cache, likely for Solr
  - There was a huge drop in 2019-07 when I changed the JVM settings
  - I think we should re-evaluate our deployment and perhaps target a different instance type and add block storage for assetstore (as we determined Linode's block storage to be too slow for Solr)

## 2020-03-17

- Update the PostgreSQL JDBC driver to version 42.2.11
- Maria from Bioversity asked me to add a new field for the combined subjects of Bioversity and CIAT, since they merged recently
  - We will use `cg.subject.alliancebiovciat`

## 2020-03-18

- Provision new Linode server (linode26) for DSpace Test to replace the current linode19 server
- Improve DSpace role of [Ansible infrastructure playbooks](https://github.com/ilri/rmg-ansible-public)
  - We should install npm packages in the DSpace user's home directory instead of globally as root

## 2020-03-19

- Finalized migration of DSpace Test to linode26 and removed linode19

## 2020-03-22

- Look over the AReS ToRs sent by Enrico and Moayad and add a few notes about missing GitHub issues
  - Hopefully now they can start working on the development!

## 2020-03-24

- Skype meeting about CGSpace with Peter and Abenet

## 2020-03-25

- I sent Atmire a message to ask if they managed to start working on the DSpace 6 port, as the last communication was twenty-six days ago when they said they were going to secure technical resources to do so
- Start adapting the `dspace` role in our [Ansible infrastructure playbooks](https://github.com/ilri/rmg-ansible-public) for DSpace 6 support

## 2020-03-26

- More work adapting the `dspace` role in our Ansible infrastructure scripts to DSpace 6
- Update Tomcat to version 7.0.103 in the Ansible infrastrcutrue playbooks and deploy on DSpace Test (linode26)
- Maria sent me a few new ORCID identifiers from Bioversity so I combined them with our existing ones, filtered the unique ones, and then resolved their names using my `resolve-orcids.py` script:

```
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcids | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2020-03-26-combined-orcids.txt
$ ./resolve-orcids.py -i /tmp/2020-03-26-combined-orcids.txt -o /tmp/2020-03-26-combined-names.txt -d
# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
```
- I checked the database for likely matches to the author name and then created a CSV with the author names and ORCID iDs:

```
dc.contributor.author,cg.creator.id
"King, Brian","Brian King: 0000-0002-7056-9214"
"Ortiz-Crespo, Berta","Berta Ortiz-Crespo: 0000-0002-6664-0815"
"Ekesa, Beatrice","Beatrice Ekesa: 0000-0002-2630-258X"
"Ekesa, B.","Beatrice Ekesa: 0000-0002-2630-258X"
"Ekesa, B.N.","Beatrice Ekesa: 0000-0002-2630-258X"
"Gullotta, G.","Gaia Gullotta: 0000-0002-2240-3869"
```

- Running the `add-orcid-identifiers-csv.py` script I added 32 ORCID iDs to items on CGSpace!

```
$ ./add-orcid-identifiers-csv.py -i /tmp/2020-03-26-ciat-orcids.csv -db dspace -u dspace -p 'fuuu'
```

- Udana from IWMI asked about some items that are missing Altmetric donuts on CGSpace
  - [One of them](https://hdl.handle.net/10568/103225) had a link to the paper on Nature, but was missing a DOI
  - [The second item](https://hdl.handle.net/10568/106899) had no donut so I [tweeted its handle](https://twitter.com/mralanorth/status/1243158045540134913)
  - [The third item](https://hdl.handle.net/10568/107258) also had no handle so I [tweeted it](https://twitter.com/mralanorth/status/1243158786392625153) as well
- Abenet pointed out [one item](https://hdl.handle.net/10568/106573) that she had tweeted last week that is missing a donut as well, so I [tweeted it](https://twitter.com/mralanorth/status/1243163710241345536) too

## 2020-03-29

- Add two more Bioversity ORCID iDs to CGSpace and then tag ~70 of the authors' existing publications in the database using this CSV with my `add-orcid-identifiers-csv.py` script:

```
dc.contributor.author,cg.creator.id
"Snook, L.K.","Laura Snook: 0000-0002-9168-1301"
"Snook, L.","Laura Snook: 0000-0002-9168-1301"
"Zheng, S.J.","Sijun Zheng: 0000-0003-1550-3738"
"Zheng, S.","Sijun Zheng: 0000-0003-1550-3738"
```

- Deploy latest Bioversity and CIAT updates on CGSpace (linode18) and DSpace Test (linode26)
- Deploy latest Ansible infrastructure playbooks on CGSpace and DSpace Test to get the latest dspace-statistics-api (v1.1.1) and Tomcat (7.0.103) versions
- Run system updates on CGSpace and DSpace Test and reboot them
  - After reboot all the Solr statistics cores came back up on the first time on both servers (yay)

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