cgspace-notes/content/post/2017-05.md

+++
date = "2017-05-01T16:21:52+02:00"
author = "Alan Orth"
title = "May, 2017"
tags = ["Notes"]

+++
## 2017-05-01

- ICARDA apparently started working on CG Core on their MEL repository
- They have done a few `cg.*` fields, but not very consistent and even copy some of CGSpace items:
    - https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full
    - https://cgspace.cgiar.org/handle/10568/73683

## 2017-05-02

- Atmire got back about the Workflow Statistics issue, and apparently it's a bug in the CUA module so they will send us a pull request

## 2017-05-04

- Sync DSpace Test with database and assetstore from CGSpace
- Re-deploy DSpace Test with Atmire's CUA patch for workflow statistics, run system updates, and restart the server
- Now I can see the workflow statistics and am able to select users, but everything returns 0 items
- Megan says there are still some mapped items are not appearing since last week, so I forced a full `index-discovery -b`
- Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace.cgiar.org/handle/10568/80731

## 2017-05-05

- Discovered that CGSpace has ~700 items that are missing the `cg.identifier.status` field
- Need to perhaps try using the "required metadata" curation task to find fields missing these items:

```
$ [dspace]/bin/dspace curate -t requiredmetadata -i 10568/1 -r - > /tmp/curation.out
```

- It seems the curation task dies when it finds an item which has missing metadata

## 2017-05-06

- Add "Blog Post" to `dc.type`
- Create ticket on Atmire tracker to ask about commissioning them to develop the feature to expose ORCID via REST/OAI: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=510
- According to the [DSpace curation docs](https://wiki.duraspace.org/display/DSDOC5x/Curation+System) the fact that the `requiredmetadata` curation task stops when it finds a missing metadata field is by design

## 2017-05-07

- Testing one replacement for CCAFS Flagships (`cg.subject.ccafs`), first changed in the submission forms, and then in the database:

```
$ ./fix-metadata-values.py -i ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu
```

- Also, CCAFS wants to re-order their flagships to prioritize the Phase II ones
- Waiting for feedback from CCAFS, then I can merge [#320](https://github.com/ilri/DSpace/pull/320)

## 2017-05-08

- Start working on CGIAR Library migration
- We decided to use AIP export to preserve the hierarchies and handles of communities and collections
- When ingesting some collections I was getting `java.lang.OutOfMemoryError: GC overhead limit exceeded`, which can be solved by disabling the GC timeout with `-XX:-UseGCOverheadLimit`
- Other times I was getting an error about heap space, so I kept bumping the RAM allocation by 512MB each time (up to 4096m!) it crashed
- This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using `dspace cleanup -v`, or else you'll run out of disk space
- In the end I realized it's better to use submission mode (`-s`) to ingest the community object as a single AIP without its children, followed by each of the collections:

```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit"
$ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done
```

- Note that in submission mode DSpace ignores the handle specified in `mets.xml` in the zip file, so you need to turn that off with `-o ignoreHandle=false`
- The `-u` option supresses prompts, to allow the process to run without user input
- Give feedback to CIFOR about their data quality:
  - Suggestion: uppercase dc.subject, cg.coverage.region, and cg.coverage.subregion in your crosswalk so they match CGSpace and therefore can be faceted / reported on easier
  - Suggestion: use CGSpace's CRP names (cg.contributor.crp), see: dspace/config/input-forms.xml
  - Suggestion: clean up duplicates and errors in funders, perhaps use a controlled vocabulary like ours, see: dspace/config/controlled-vocabularies/dc-description-sponsorship.xml
  - Suggestion: use dc.type "Blog Post" instead of "Blog" for your blog post items (we are also adding a "Blog Post" type to CGSpace soon)
  - Question: many of your items use dc.document.uri AND cg.identifier.url with the same text value?
- Help Marianne from WLE with an Open Search query to show the latest WLE CRP outputs: https://cgspace.cgiar.org/open-search/discover?query=crpsubject:WATER%2C+LAND+AND+ECOSYSTEMS&sort_by=2&order=DESC
- This uses the webui's item list sort options, see `webui.itemlist.sort-option` in `dspace.cfg`
- The equivalent Discovery search would be: https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=WATER%2C+LAND+AND+ECOSYSTEMS&submit_apply_filter=&query=&rpp=10&sort_by=dc.date.issued_dt&order=desc

## 2017-05-09

- The CGIAR Library metadata has some blank metadata values, which leads to `|||` in the Discovery facets
- Clean these up in the database using:

```
dspace=# delete from metadatavalue where resource_type_id=2 and text_value=''
```

- I ended up running into issues during data cleaning and decided to wipe out the entire community and re-sync DSpace Test assetstore and database from CGSpace rather than waiting for the cleanup task to clean up
- Hours into the re-ingestion I ran into more errors, and had to erase everything and start over _again_!
- Now, no matter what I do I keep getting foreign key errors...

```
Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey"
  Detail: Key (handle_id)=(80928) already exists.
```

- I think those errors actually come from me running the `update-sequences.sql` script while Tomcat/DSpace are running
- Apparently you need to stop Tomcat!

## 2017-05-10

- Atmire says they are willing to extend the ORCID implementation, and I've asked them to provide a quote
- I clarified that the scope of the implementation should be that ORCIDs are stored in the database and exposed via REST / API like other fields
- Finally finished importing all the CGIAR Library content, final method was:

```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit"
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2517/10947-2517.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2515/10947-2515.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2516/10947-2516.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ [dspace]/bin/dspace packager -s -t AIP -o ignoreHandle=false -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done
```

- Basically, import the smaller communities using recursive AIP import (with `skipIfParentMissing`)
- Then, for the larger collection, create the community, collections, and items separately, ingesting the items one by one
- The `-XX:-UseGCOverheadLimit` JVM option helps with some issues in large imports
- After this I ran the `update-sequences.sql` script (with Tomcat shut down), and cleaned up the 200+ blank metadata records:

```
dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
```

## 2017-05-13

- After quite a bit of troubleshooting with importing cleaned up data as CSV, it seems that there are actually [NUL](https://en.wikipedia.org/wiki/Null_character) characters in the `dc.description.abstract` field (at least) on the lines where CSV importing was failing
- I tried to find a way to remove the characters in vim or Open Refine, but decided it was quicker to just remove the column temporarily and import it
- The import was successful and detected 2022 changes, which should likely be the rest that were failing to import before

## 2017-05-15

- To delete the blank lines that cause isses during import we need to use a regex in vim `g/^$/d`
- After that I started looking in the `dc.subject` field to try to pull countries and regions out, but there are too many values in there
- Bump the Academicons dependency of the Mirage 2 themes from 1.6.0 to 1.8.0 because the upstream deleted the old tag and now the build is failing: [#321](https://github.com/ilri/DSpace/pull/321)
- Merge changes to CCAFS project identifiers and flagships: [#320](https://github.com/ilri/DSpace/pull/320)
- Run updates for CCCAFS flagships on CGSpace:

```
$ ./fix-metadata-values.py -i /tmp/ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p 'fuuu'
```

- These include:
  - GENDER AND SOCIAL DIFFERENTIATION→GENDER AND SOCIAL INCLUSION
  - MANAGING CLIMATE RISK→CLIMATE SERVICES AND SAFETY NETS

- Re-deploy CGSpace and DSpace Test and run system updates
- Reboot DSpace Test
- Fix cron jobs for log management on DSpace Test, as they weren't catching `dspace.log.*` files correctly and we had over six months of them and they were taking up many gigs of disk space

## 2017-05-16

- Discuss updates to WLE themes for their Phase II
- Make an issue to track the changes to `cg.subject.wle`: [#322](https://github.com/ilri/DSpace/issues/322)

## 2017-05-17

- Looking into the error I get when trying to create a new collection on DSpace Test:

```
ERROR: duplicate key value violates unique constraint "handle_pkey" Detail: Key (handle_id)=(84834) already exists.
```

- I tried updating the sequences a few times, with Tomcat running and stopped, but it hasn't helped
- It appears item with `handle_id` 84834 is one of the imported CGIAR Library items:

```
dspace=# select * from handle where handle_id=84834;
 handle_id |   handle   | resource_type_id | resource_id
-----------+------------+------------------+-------------
     84834 | 10947/1332 |                2 |       87113
```

- Looks like the max `handle_id` is actually much higher:

```
dspace=# select * from handle where handle_id=(select max(handle_id) from handle);
 handle_id |  handle  | resource_type_id | resource_id
-----------+----------+------------------+-------------
     86873 | 10947/99 |                2 |       89153
(1 row)
```

- I've posted on the dspace-test mailing list to see if I can just manually set the `handle_seq` to that value