## June, 2017

Thu Jun 01, 2017 in Notes

## 2017-06-01

- After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes
- The `cg.identifier.wletheme` field will be used for both Phase I and Phase II Research Themes
- Then we’ll create a new sub-community for Phase II and create collections for the research themes there
- The current “Research Themes” community will be renamed to “WLE Phase I Research Themes”
- Tagged all items in the current Phase I collections with their appropriate themes
- Create pull request to add Phase II research themes to the submission form: #328
- Add `cg.subject.system` to CGSpace metadata registry, for subject from the upcoming CGIAR Library migration

## 2017-06-04

- After adding `cg.identifier.wletheme` to 1106 WLE items I can see the field on XMLUI but not in REST!
- Strangely it happens on DSpace Test AND on CGSpace!
- I tried to re-index Discovery but it didn’t fix it
- Run all system updates on DSpace Test and reboot the server
- After rebooting the server (and therefore restarting Tomcat) the new metadata field is available
- I’ve sent a message to the dspace-tech mailing list to ask if this is a bug and whether I should file a Jira ticket

## 2016-06-05

- Rename WLE’s “Research Themes” sub-community to “WLE Phase I Research Themes” on DSpace Test so Macaroni Bros can continue their testing
- Macaroni Bros tested it and said it’s fine, so I renamed it on CGSpace as well
- Working on how to automate the extraction of the CIAT Book chapters, doing some magic in OpenRefine to extract page from–to from cg.identifier.url and dc.format.extent, respectively:
  - cg.identifier.url: `value.split("page=", "")[1]`
  - dc.format.extent: `value.replace("p. ", "").split("-")[1].toNumber() - value.replace("p. ", "").split("-")[0].toNumber()`
- Finally, after some filtering to see which small outliers there were (based on dc.format.extent using “p. 1-14” vs “29 p."), create a new column with last page number:
  - `cells["dc.page.from"].value.toNumber() + cells["dc.format.pages"].value.toNumber()`
- Then create a new, unique file name to be used in the output, based on a SHA1 of the dc.title and with a description:
  - dc.page.to: `value.split(" ")[0].replace(",","").toLowercase() + "-" + sha1(value).get(1,9) + ".pdf__description:" + cells["dc.type"].value`
- Start processing 769 records after filtering the following (there are another 159 records that have some other format, or for example they have their own PDF which I will process later), using a modified `generate-thumbnails.py` script to read certain fields and then pass to GhostScript:
  - cg.identifier.url: `value.contains("page=")`
  - dc.format.extent: `or(value.contains("p. "),value.contains(" p."))`
  - Command like: `$ gs -dNOPAUSE -dBATCH -dFirstPage=14 -dLastPage=27 -sDEVICE=pdfwrite -sOutputFile=beans.pdf -f 12605-1.pdf`
- 17 of the items have issues with incorrect page number ranges, and upon closer inspection they do not appear in the referenced PDF
- I’ve flagged them and proceeded without them (752 total) on DSpace Test:

    $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/93843 --source /home/aorth/src/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books.map &> /tmp/ciat-books.log

- I went and did some basic sanity checks on the remaining items in the CIAT Book Chapters and decided they are mostly fine (except one duplicate and the flagged ones), so I imported them to DSpace Test too (162 items)
- Total items in CIAT Book Chapters is 914, with the others being flagged for some reason, and we should send that back to CIAT
- Restart Tomcat on CGSpace so that the `cg.identifier.wletheme` field is available on REST API for Macaroni Bros

## 2017-06-07

- Testing Atmire’s patch for the CUA Workflow Statistics again
- Still doesn’t seem to give results I’d expect, like there are no results for Maria Garruccio, or for the ILRI community!
- Then I’ll file an update to the issue on Atmire’s tracker
- Created a new branch with just the relevant changes, so I can send it to them
- One thing I noticed is that there is a failed database migration related to CUA:

    +----------------+----------------------------+---------------------+---------+
    | Version        | Description                | Installed on        | State   |
    +----------------+----------------------------+---------------------+---------+
    | 1.1            | Initial DSpace 1.1 databas |                     | PreInit |
    | 1.2            | Upgrade to DSpace 1.2 sche |                     | PreInit |
    | 1.3            | Upgrade to DSpace 1.3 sche |                     | PreInit |
    | 1.3.9          | Drop constraint for DSpace |                     | PreInit |
    | 1.4            | Upgrade to DSpace 1.4 sche |                     | PreInit |
    | 1.5            | Upgrade to DSpace 1.5 sche |                     | PreInit |
    | 1.5.9          | Drop constraint for DSpace |                     | PreInit |
    | 1.6            | Upgrade to DSpace 1.6 sche |                     | PreInit |
    | 1.7            | Upgrade to DSpace 1.7 sche |                     | PreInit |
    | 1.8            | Upgrade to DSpace 1.8 sche |                     | PreInit |
    | 3.0            | Upgrade to DSpace 3.x sche |                     | PreInit |
    | 4.0            | Initializing from DSpace 4 | 2015-11-20 12:42:52 | Success |
    | 5.0.2014.08.08 | DS-1945 Helpdesk Request a | 2015-11-20 12:42:53 | Success |
    | 5.0.2014.09.25 | DS 1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
    | 5.0.2014.09.26 | DS-1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
    | 5.0.2015.01.27 | MigrateAtmireExtraMetadata | 2015-11-20 12:43:29 | Success |
    | 5.0.2017.04.28 | CUA eperson metadata migra | 2017-06-07 11:07:28 | OutOrde |
    | 5.5.2015.12.03 | Atmire CUA 4 migration     | 2016-11-27 06:39:05 | OutOrde |
    | 5.5.2015.12.03 | Atmire MQM migration       | 2016-11-27 06:39:06 | OutOrde |
    | 5.6.2016.08.08 | CUA emailreport migration  | 2017-01-29 11:18:56 | OutOrde |
    +----------------+----------------------------+---------------------+---------+

- Merge the pull request for WLE Phase II themes

## 2017-06-18

- Redeploy CGSpace with latest changes from `5_x-prod`, run system updates, and reboot the server
- Continue working on ansible infrastructure changes for CGIAR Library

## 2017-06-20

- Import Abenet and Peter’s changes to the CGIAR Library CRP community
- Due to them using Windows and renaming some columns there were formatting, encoding, and duplicate metadata value issues
- I had to remove some fields from the CSV and rename some back to, ie, `dc.subject[en_US]` just so DSpace would detect changes properly
- Now it looks much better: https://dspacetest.cgiar.org/handle/10947/2517
- Removing the HTML tags and HTML/XML entities using the following GREL:
  - `replace(value,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')`
  - `value.unescape("html").unescape("xml")`
- Finally import 914 CIAT Book Chapters to CGSpace in two batches:

    $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/35701 --source /home/aorth/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books.map &> /tmp/ciat-books.log
    $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/35701 --source /home/aorth/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books2.map &> /tmp/ciat-books2.log

## 2017-06-25

- WLE has said that one of their Phase II research themes is being renamed from `Regenerating Degraded Landscapes` to `Restoring Degraded Landscapes`
- Pull request with the changes to `input-forms.xml`: #329
- As of now it doesn’t look like there are any items using this research theme so we don’t need to do any updates:

    dspace=# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=237 and text_value like 'Regenerating Degraded Landscapes%';
     text_value
    ------------
    (0 rows)

- Marianne from WLE asked if they can have both Phase I and II research themes together in the item submission form
- Perhaps we can add them together in the same question for `cg.identifier.wletheme`

## 2017-06-30

- CGSpace went down briefly, I see lots of these errors in the dspace logs:

    Java stacktrace: java.util.NoSuchElementException: Timeout waiting for idle object

- After looking at the Tomcat logs, Munin graphs, and PostgreSQL connection stats, it seems there is just a high load
- Might be a good time to adjust DSpace’s database connection settings, like I first mentioned in April, 2017 after reading the 2017-04 DCAT comments
- I’ve adjusted the following in CGSpace’s config:
  - `db.maxconnections` 30→70 (the default PostgreSQL config allows 100 connections, so DSpace’s default of 30 is quite low)
  - `db.maxwait` 5000→10000
  - `db.maxidle` 8→20 (DSpace default is -1, unlimited, but we had set it to 8 earlier)
- We will need to adjust this again (as well as the `pg_hba.conf` settings) when we deploy tsega’s REST API
- Whip up a test for Marianne of WLE to be able to show both their Phase I and II research themes in the CGSpace item submission form: