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146 lines
9.6 KiB
Markdown
146 lines
9.6 KiB
Markdown
+++
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date = "2017-06-01T10:14:52+03:00"
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author = "Alan Orth"
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title = "June, 2017"
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tags = ["Notes"]
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+++
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## 2017-06-01
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- After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes
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- The `cg.identifier.wletheme` field will be used for both Phase I and Phase II Research Themes
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- Then we'll create a new sub-community for Phase II and create collections for the research themes there
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- The current "Research Themes" community will be renamed to "WLE Phase I Research Themes"
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- Tagged all items in the current Phase I collections with their appropriate themes
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- Create pull request to add Phase II research themes to the submission form: [#328](https://github.com/ilri/DSpace/pull/328)
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- Add `cg.subject.system` to CGSpace metadata registry, for subject from the upcoming CGIAR Library migration
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## 2017-06-04
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- After adding `cg.identifier.wletheme` to 1106 WLE items I can see the field on XMLUI but not in REST!
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- Strangely it happens on DSpace Test AND on CGSpace!
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- I tried to re-index Discovery but it didn't fix it
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- Run all system updates on DSpace Test and reboot the server
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- After rebooting the server (and therefore restarting Tomcat) the new metadata field is available
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- 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
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## 2016-06-05
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- Rename WLE's "Research Themes" sub-community to "WLE Phase I Research Themes" on DSpace Test so Macaroni Bros can continue their testing
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- Macaroni Bros tested it and said it's fine, so I renamed it on CGSpace as well
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- 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:
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- cg.identifier.url: `value.split("page=", "")[1]`
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- dc.format.extent: `value.replace("p. ", "").split("-")[1].toNumber() - value.replace("p. ", "").split("-")[0].toNumber()`
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- 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:
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- `cells["dc.page.from"].value.toNumber() + cells["dc.format.pages"].value.toNumber()`
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- 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:
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- dc.page.to: `value.split(" ")[0].replace(",","").toLowercase() + "-" + sha1(value).get(1,9) + ".pdf__description:" + cells["dc.type"].value`
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- 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:
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- cg.identifier.url: `value.contains("page=")`
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- dc.format.extent: `or(value.contains("p. "),value.contains(" p."))`
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- Command like: `$ gs -dNOPAUSE -dBATCH -dFirstPage=14 -dLastPage=27 -sDEVICE=pdfwrite -sOutputFile=beans.pdf -f 12605-1.pdf`
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- 17 of the items have issues with incorrect page number ranges, and upon closer inspection they do not appear in the referenced PDF
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- I've flagged them and proceeded without them (752 total) on DSpace Test:
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```
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$ 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
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```
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- 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)
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- Total items in CIAT Book Chapters is 914, with the others being flagged for some reason, and we should send that back to CIAT
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- Restart Tomcat on CGSpace so that the `cg.identifier.wletheme` field is available on REST API for Macaroni Bros
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## 2017-06-07
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- Testing [Atmire's patch for the CUA Workflow Statistics again](https://github.com/ilri/DSpace/pull/319)
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- Still doesn't seem to give results I'd expect, like there are no results for Maria Garruccio, or for the ILRI community!
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- Then I'll file an update to the issue on Atmire's tracker
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- Created a new branch with just the relevant changes, so I can send it to them
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- One thing I noticed is that there is a failed database migration related to CUA:
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```
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+----------------+----------------------------+---------------------+---------+
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| Version | Description | Installed on | State |
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+----------------+----------------------------+---------------------+---------+
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| 1.1 | Initial DSpace 1.1 databas | | PreInit |
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| 1.2 | Upgrade to DSpace 1.2 sche | | PreInit |
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| 1.3 | Upgrade to DSpace 1.3 sche | | PreInit |
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| 1.3.9 | Drop constraint for DSpace | | PreInit |
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| 1.4 | Upgrade to DSpace 1.4 sche | | PreInit |
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| 1.5 | Upgrade to DSpace 1.5 sche | | PreInit |
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| 1.5.9 | Drop constraint for DSpace | | PreInit |
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| 1.6 | Upgrade to DSpace 1.6 sche | | PreInit |
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| 1.7 | Upgrade to DSpace 1.7 sche | | PreInit |
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| 1.8 | Upgrade to DSpace 1.8 sche | | PreInit |
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| 3.0 | Upgrade to DSpace 3.x sche | | PreInit |
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| 4.0 | Initializing from DSpace 4 | 2015-11-20 12:42:52 | Success |
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| 5.0.2014.08.08 | DS-1945 Helpdesk Request a | 2015-11-20 12:42:53 | Success |
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| 5.0.2014.09.25 | DS 1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
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| 5.0.2014.09.26 | DS-1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
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| 5.0.2015.01.27 | MigrateAtmireExtraMetadata | 2015-11-20 12:43:29 | Success |
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| 5.0.2017.04.28 | CUA eperson metadata migra | 2017-06-07 11:07:28 | OutOrde |
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| 5.5.2015.12.03 | Atmire CUA 4 migration | 2016-11-27 06:39:05 | OutOrde |
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| 5.5.2015.12.03 | Atmire MQM migration | 2016-11-27 06:39:06 | OutOrde |
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| 5.6.2016.08.08 | CUA emailreport migration | 2017-01-29 11:18:56 | OutOrde |
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+----------------+----------------------------+---------------------+---------+
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```
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- Merge the pull request for [WLE Phase II themes](https://github.com/ilri/DSpace/pull/328)
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## 2017-06-18
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- Redeploy CGSpace with latest changes from `5_x-prod`, run system updates, and reboot the server
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- Continue working on ansible infrastructure changes for CGIAR Library
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## 2017-06-20
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- Import Abenet and Peter's changes to the CGIAR Library CRP community
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- Due to them using Windows and renaming some columns there were formatting, encoding, and duplicate metadata value issues
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- 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
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- Now it looks much better: https://dspacetest.cgiar.org/handle/10947/2517
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- Removing the HTML tags and HTML/XML entities using the following GREL:
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- `replace(value,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')`
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- `value.unescape("html").unescape("xml")`
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- Finally import 914 CIAT Book Chapters to CGSpace in two batches:
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```
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$ 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
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$ 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
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```
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## 2017-06-25
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- WLE has said that one of their Phase II research themes is being renamed from `Regenerating Degraded Landscapes` to `Restoring Degraded Landscapes`
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- Pull request with the changes to `input-forms.xml`: [#329](https://github.com/ilri/DSpace/pull/329)
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- 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:
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```
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dspace=# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=237 and text_value like 'Regenerating Degraded Landscapes%';
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text_value
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------------
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(0 rows)
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```
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- Marianne from WLE asked if they can have both Phase I and II research themes together in the item submission form
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- Perhaps we can add them together in the same question for `cg.identifier.wletheme`
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## 2017-06-30
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- CGSpace went down briefly, I see lots of these errors in the dspace logs:
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```
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Java stacktrace: java.util.NoSuchElementException: Timeout waiting for idle object
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```
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- After looking at the Tomcat logs, Munin graphs, and PostgreSQL connection stats, it seems there is just a high load
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- 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](https://wiki.lyrasis.org/display/cmtygp/DCAT+Meeting+April+2017)
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- I've adjusted the following in CGSpace's config:
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- `db.maxconnections` 30→70 (the default PostgreSQL config allows 100 connections, so DSpace's default of 30 is quite low)
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- `db.maxwait` 5000→10000
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- `db.maxidle` 8→20 (DSpace default is -1, unlimited, but we had set it to 8 earlier)
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- We will need to adjust this again (as well as the `pg_hba.conf` settings) when we deploy tsega's REST API
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- 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:
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