cgspace-notes/content/posts/2019-07.md

---
title: "July, 2019"
date: 2019-07-01T12:13:51+03:00
author: "Alan Orth"
tags: ["Notes"]
---

## 2019-07-01

- Create an "AfricaRice books and book chapters" collection on CGSpace for AfricaRice
- Last month Sisay asked why the following "most popular" statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
  - [DSpace Test](https://dspacetest.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&time_filter_end_date=01%2F12%2F2018)
  - [CGSpace](https://cgspace.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&time_filter_end_date=01%2F12%2F2018)
- Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community

<!--more-->

- If I change the parameters to 2019 I see stats, so I'm really thinking it has something to do with the sharded yearly Solr statistics cores
  - I checked the Solr admin UI and I see all Solr cores loaded, so I don't know what it could be
  - When I check the Atmire content and usage module it seems obvious that there is a problem with the old cores because I dont have anything before 2019-01

![Atmire CUA 2018 stats missing](/cgspace-notes/2019/07/atmire-cua-2018-missing.png)

- I don't see anyone logged in right now so I'm going to try to restart Tomcat and see if the stats are accessible after Solr comes back up
- I decided to run all system updates on the server (linode18) and reboot it
  - After rebooting Tomcat came back up, but the the Solr statistics cores were not all loaded
  - The error is always (with a different core):

```
org.apache.solr.common.SolrException: Error CREATEing SolrCore 'statistics-2010': Unable to create core [statistics-2010] Caused by: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2010/data/index/write.lock
```

- I restarted Tomcat *ten times* and it never worked...
- I tried to stop Tomcat and delete the write locks:

```
# systemctl stop tomcat7
# find /dspace/solr/statistics* -iname "*.lock" -print -delete
/dspace/solr/statistics/data/index/write.lock
/dspace/solr/statistics-2010/data/index/write.lock
/dspace/solr/statistics-2011/data/index/write.lock
/dspace/solr/statistics-2012/data/index/write.lock
/dspace/solr/statistics-2013/data/index/write.lock
/dspace/solr/statistics-2014/data/index/write.lock
/dspace/solr/statistics-2015/data/index/write.lock
/dspace/solr/statistics-2016/data/index/write.lock
/dspace/solr/statistics-2017/data/index/write.lock
/dspace/solr/statistics-2018/data/index/write.lock
# find /dspace/solr/statistics* -iname "*.lock" -print -delete
# systemctl start tomcat7
```

- But it still didn't work!
- I stopped Tomcat, deleted the old locks, and will try to use the "simple" lock file type in `solr/statistics/conf/solrconfig.xml`:

```
<lockType>${solr.lock.type:simple}</lockType>
```

- And after restarting Tomcat it still doesn't work
- Now I'll try going back to "native" locking with `unlockAtStartup`:

```
<unlockOnStartup>true</unlockOnStartup>
```

- Now the cores seem to load, but I still see an error in the Solr Admin UI and I still can't access any stats before 2018
- I filed an [issue with Atmire](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685), so let's see if they can help
- And since I'm annoyed and it's been a few months, I'm going to move the JVM heap settings that I've been testing on DSpace Test to CGSpace
- The old ones were:

```
-Djava.awt.headless=true -Xms8192m -Xmx8192m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=5400 -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false
```

- And the new ones come from Solr 4.10.x's startup scripts:

```
    -Djava.awt.headless=true
    -Xms8192m -Xmx8192m
    -Dfile.encoding=UTF-8
    -XX:NewRatio=3
    -XX:SurvivorRatio=4
    -XX:TargetSurvivorRatio=90
    -XX:MaxTenuringThreshold=8
    -XX:+UseConcMarkSweepGC
    -XX:+UseParNewGC
    -XX:ConcGCThreads=4 -XX:ParallelGCThreads=4
    -XX:+CMSScavengeBeforeRemark
    -XX:PretenureSizeThreshold=64m
    -XX:+UseCMSInitiatingOccupancyOnly
    -XX:CMSInitiatingOccupancyFraction=50
    -XX:CMSMaxAbortablePrecleanTime=6000
    -XX:+CMSParallelRemarkEnabled
    -XX:+ParallelRefProcEnabled
    -Dcom.sun.management.jmxremote
    -Dcom.sun.management.jmxremote.port=1337
    -Dcom.sun.management.jmxremote.ssl=false
    -Dcom.sun.management.jmxremote.authenticate=false
```

## 2019-07-02

- Help upload twenty-seven posters from the 2019-05 Sharefair to CGSpace
  - Sisay had already done the SAFBundle so I did some minor corrections to and uploaded them to a temporary collection so I could check them in OpenRefine:

```
$ sed -i 's/CC-BY 4.0/CC-BY-4.0/' item_*/dublin_core.xml
$ echo "10568/101992" >> item_*/collections
$ dspace import -a -e me@cgiar.org -m 2019-07-02-Sharefair.map -s /tmp/Sharefair_mapped
```
- I noticed that all twenty-seven items had double dates like "2019-05||2019-05" so I fixed those, but the rest of the metadata looked good so I unmapped them from the temporary collection
- Finish looking at the fifty-six AfricaRice items and upload them to CGSpace: 

```
$ dspace import -a -e me@cgiar.org -m 2019-07-02-AfricaRice-11to73.map -s /tmp/SimpleArchiveFormat
```

- Peter pointed out that the Sharefair dates I fixed were not actually fixed
  - It seems there is a bug that causes DSpace to not detect changes if the values are the same like "2019-05||2019-05" and you try to remove one
  - To get it to work I had to change some of them to 2019-01, then remove them

## 2019-07-03

- Atmire responded about the [Solr issue](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685) and said they would be willing to help

## 2019-07-04

- Maria Garruccio sent me some new ORCID identifiers for Bioversity authors
  - I combined them with our existing list and then used my `resolve-orcids.py` script to update the names from ORCID.org:

```
$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/new-bioversity-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2019-07-04-orcid-ids.txt
$ ./resolve-orcids.py -i /tmp/2019-07-04-orcid-ids.txt -o 2019-07-04-orcid-names.txt -d
```

- Send and merge a pull request for the new ORCID identifiers ([#428](https://github.com/ilri/DSpace/pull/428))
- I created a CSV with some ORCID identifiers that I had seen change so I could update any existing ones in the databse:

```
cg.creator.id,correct
"Marius Ekué: 0000-0002-5829-6321","Marius R.M. Ekué: 0000-0002-5829-6321"
"Mwungu: 0000-0001-6181-8445","Chris Miyinzi Mwungu: 0000-0001-6181-8445"
"Mwungu: 0000-0003-1658-287X","Chris Miyinzi Mwungu: 0000-0003-1658-287X"
```

- But when I ran `fix-metadata-values.py` I didn't see any changes:

```
$ ./fix-metadata-values.py -i 2019-07-04-update-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -m 240 -t correct -d
```

## 2019-07-06

- Send a reminder to Marie about my notes on the [CG Core v2 issue I created two weeks ago](https://github.com/AgriculturalSemantics/cg-core/issues/2)

## 2019-07-08

- Communicate with Atmire about the Solr statistics cores issue
  - I suspect we might need to get more disk space on DSpace Test so we can try to replicate the production environment more closely
- Meeting with AgroKnow and CTA about their new ICT Update story telling thing
  - AgroKnow has developed a React application to display tag clouds based on harvesting metadata and full text from CGSpace items
  - We discussed how to host it technically, perhaps we purchase a server to run it on and just give AgroKnow guys access
- Playing with the idea of using [xsv](https://github.com/BurntSushi/xsv) to do some basic batch quality checks on CSVs, for example to find items that might be duplicates if they have the same DOI or title:

```
$ xsv frequency --select cg.identifier.doi --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E ',1'
field,value,count
cg.identifier.doi,https://doi.org/10.1016/j.agwat.2018.06.018,2
$ xsv frequency --select dc.title --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E ',1'         
field,value,count
dc.title,Reference evapotranspiration prediction using hybridized fuzzy model with firefly algorithm: Regional case study in Burkina Faso,2
```

- Or perhaps if DOIs are valid or not (having doi.org in the URL):

```
$ xsv frequency --select cg.identifier.doi --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E 'doi.org'
field,value,count
cg.identifier.doi,https://hdl.handle.net/10520/EJC-1236ac700f,1
```

- Or perhaps items with invalid ISSNs (according to the [ISSN code format](https://en.wikipedia.org/wiki/International_Standard_Serial_Number#Code_format)):

```
$ xsv select dc.identifier.issn cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v '"' | grep -v -E '^[0-9]{4}-[0-9]{3}[0-9xX]$'
dc.identifier.issn
978-3-319-71997-9
978-3-319-71997-9
978-3-319-71997-9
978-3-319-58789-9
2320-7035 
 2593-9173
```

## 2019-07-09

- Thinking about data cleaning automation again and found some resources about Python and Pandas:
  - https://realpython.com/python-data-cleaning-numpy-pandas/
  - https://mode.com/blog/python-data-cleaning-libraries

## 2019-07-11

- Skype call with Marie Angelique about CG Core v2
  - We discussed my comments and suggestions from last week
  - One comment she had was that we should try to move our center-specific subjects into `DCTERMS.subject` and normalize them against AGROVOC
  - I updated my [gist about CGSpace metadata changes](https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409)
- Skype call with Jane Poole to discuss OpenRXV/AReS Phase II TORs
  - I need to follow up with Moayad about the reporting functionality
  - Also, I need to email Harrison my notes on the CG Core v2 stuff
  - Also, Jane asked me to check the Data Portal to see which email address requests for confidential data are going
- Yesterday Theirry from CTA asked me about an error he was getting while submitting an item on CGSpace: "Unable to load Submission Information, since WorkspaceID (ID:S106658) is not a valid in-process submission."
- I looked in the DSpace logs and found this right around the time of the screenshot he sent me:

```
2019-07-10 11:50:27,433 INFO  org.dspace.submit.step.CompleteStep @ lewyllie@cta.int:session_id=A920730003BCAECE8A3B31DCDE11A97E:submission_complete:Completed submission with id=106658
```

- I'm assuming something happened in his browser (like a refresh) after the item was submitted...

## 2019-07-12

- Atmire responded with some initial feedback about our Tomcat configuration related to the [Solr issue I raised recently](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685)
  - Unfortunately there is no concrete feedback yet
  - I think we need to upgrade our DSpace Test server so we can fit all the Solr cores...
  - Actually, I looked and there were over 40 GB free on DSpace Test so I copied the Solr statistics cores for the years 2017 to 2010 from CGSpace to DSpace Test because they weren't actually very large
  - I re-deployed DSpace for good measure, and I think all Solr cores are loading... I will do more tests later
- Run all system updates on DSpace Test (linode19) and reboot it
- Try to run `dspace cleanup -v` on CGSpace and ran into an error:

```
Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
  Detail: Key (bitstream_id)=(167394) is still referenced from table "bundle".
```

- The solution is, as always:

```
# su - postgres
$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (167394);'
UPDATE 1
```

## 2019-07-16

- Completely reset the Podman configuration on my laptop because there were some layers that I couldn't delete and it had been some time since I did a cleanup:

```
$ podman system prune -a -f --volumes
$ sudo rm -rf ~/.local/share/containers
```

- Then pull a new PostgreSQL 9.6 image and load a CGSpace database dump into a new local test container:

```
$ podman pull postgres:9.6-alpine
$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
$ createuser -h localhost -U postgres --pwprompt dspacetest
$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost ~/Downloads/cgspace_2019-07-16.backup
$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'                     
$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
```

- Start working on implementing the [CG Core v2 changes](https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409) on my local DSpace test environment
- Make a pull request to CG Core v2 with some fixes for typos in the specification ([#5](https://github.com/AgriculturalSemantics/cg-core/pull/5))

## 2019-07-18

- Talk to Moayad about the remaining issues for OpenRXV / AReS
  - He sent a pull request with some changes for the bar chart and documentation about configuration, and said he'd finish the export feature next week
- Sisay said a user was having problems registering on CGSpace and it looks like the email account expired again:

```
$ dspace test-email

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

Error sending email:
 - Error: javax.mail.AuthenticationFailedException

Please see the DSpace documentation for assistance.
```

- I emailed ICT to ask them to reset it and make the expiration period longer if possible

## 2019-07-19

- ICT reset the password for the CGSpace support account and apparently removed the expiry requirement
  - I tested the account and it's working

## 2019-07-20

- Create an account for Lionelle Samnick on CGSpace because the registration isn't working for some reason:

```
$ dspace user --add --givenname Lionelle --surname Samnick --email blah@blah.com --password 'blah'
```

- I added her as a submitter to [CTA ISF Pro-Agro series](https://cgspace.cgiar.org/handle/10568/74536)
- Start looking at 1429 records for the Bioversity batch import
  - Multiple authors should be specified with multi-value separatator (||) instead of ;
  - We don't use "(eds)" as an author
  - Same issue with dc.publisher using ";" for multiple values
  - Some invalid ISSNs in dc.identifier.issn (they look like ISBNs)
  - I see some ISSNs in the dc.identifier.isbn field
  - I see some invalid ISBNs that look like Excel errors (9,78E+12)
  - For DOI we just use the URL, not "DOI: https://doi.org..."
  - I see an invalid "LEAVE BLANK" in the cg.contributor.crp field
  - Country field is using "," for multiple values instead of "||"
  - Region field is using "," for multiple values instead of "||"
  - Language field should be lowercase like "en", and it is using the wrong multiple value separator, and has some invalid values
  - What is the cg.identifier.url2 field? You should probably add those as cg.link.reference

## 2019-07-22

- Raise an [issue on CG Core v2 spec regarding country and region coverage](https://github.com/AgriculturalSemantics/cg-core/issues/8)
  - The current standard has them implemented as a class like this:

```
    <dct:coverage>
        <dct:spatial>
            <type>Country</type>
            <dct:identifier>http://sws.geonames.org/192950</dct:identifier>
            <rdfs:label>Kenya</rdfs:label>
        </dct:spatial>
    </dct:coverage>
```

- I left a note saying that DSpace is technically limited to a flat schema so we use `cg.coverage.country: Kenya`
- Do a little more work on CG Core v2 in the input forms

## 2019-07-25

- Generate a list of the ORCID identifiers that we added to CGSpace in 2019 for Sara Jani at ICARDA
- Bioversity sent a new file for their migration to CGSpace
  - There is always a blank row and blank column at the end
  - One invalid type (Brie)
  - 824 items with leading/trailing spaces in dc.identifier.citation
  - 175 items with a trailing comma in dc.identifier.citation (using custom text facet with GREL `value.endsWith(',').toString()`)
  - Fix them with GREL transform: `value.replace(/,$/, '')`
  - A few strange publishers after splitting multi-value cells, like "(Belgium)"
  - Deleted four ISSNs that are actually ISBNs and are already present in the ISBN field
  - Eight invalid ISBNs 
  - Convert all DOIs to "https://doi.org" format and fix one invalid DOI
  - Fix a handful of incorrect CRPs that seem to have been split on comma ","
  - Lots of strange values in cg.link.reference, and I normalized all DOIs to https://doi.org format
    - There are lots of invalid links here, like "36" and "recordlink:publications:2606" and "t3://record?identifier=publications&amp;uid=2606"
    - Also there are hundreds of items that use the same value for cg.link.reference AND cg.link.dataurl
  - Use https:// for all Bioversity links (reference, data url, permalink)

- I might be able to use [isbnlib](https://pypi.org/project/isbnlib/) to validate ISBNs in Python:

```
if isbnlib.is_isbn10('9966-955-07-0') or isbnlib.is_isbn13('9966-955-07-0'):
    print("Yes")
else:
    print("No")
```

- Or with [python-stdnum](https://github.com/arthurdejong/python-stdnum):

```
from stdnum import isbn
from stdnum import issn

isbn.validate('978-92-9043-389-7')
issn.validate('1020-3362')
```

## 2019-07-26

- Bioversity sent me an updated CSV file that fixes some of the issues I pointed out yesterday
  - There are still 1429 records
  - There are still one extra row and one extra column
  - There are still eight invalid ISBNs (according to my `validate.py` script)

- I figured out a GREL to trim spaces in multi-value cells without splitting them: 

```
value.replace(/\s+\|\|/,"||").replace(/\|\|\s+/,"||")
```

- I whipped up a quick script using Python Pandas to do whitespace cleanup

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