CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

June, 2017

by Alan Orth in  

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:

Test A for displaying the Phase I and II research themes Test B for displaying the Phase I and II research themes