## March, 2017

Wed Mar 01, 2017 in Notes

## 2017-03-01

- Run the 279 CIAT author corrections on CGSpace

## 2017-03-02

- Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
- CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
- They might come in at the top level in one “CGIAR System” community, or with several communities
- I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?
- Need to send Peter and Michael some notes about this in a few days
- Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
- Filed an issue on DSpace issue tracker for the `filter-media` bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: DS-3516
- Discovered that the ImageMagic `filter-media` plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
- Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see 10568/51999):

    $ identify ~/Desktop/alc_contrastes_desafios.jpg
    /Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000

- This results in discolored thumbnails when compared to the original PDF, for example sRGB and CMYK:

- I filed an issue for the color space thing: DS-3517

## 2017-03-03

- I created a patch for DS-3517 and made a pull request against upstream `dspace-5_x`: https://github.com/DSpace/DSpace/pull/1669
- Looks like `-colorspace sRGB` alone isn’t enough, we need to use profiles:

    $ convert alc_contrastes_desafios.pdf\[0\] -profile /opt/brew/Cellar/ghostscript/9.20/share/ghostscript/9.20/iccprofiles/default_cmyk.icc -thumbnail 300x300 -flatten -profile /opt/brew/Cellar/ghostscript/9.20/share/ghostscript/9.20/iccprofiles/default_rgb.icc alc_contrastes_desafios.pdf.jpg

- This reads the input file, applies the CMYK profile, applies the RGB profile, then writes the file
- Note that you should set the first profile immediately after the input file
- Also, it is better to use profiles than setting `-colorspace`
- This is a great resource describing the color stuff: http://www.imagemagick.org/Usage/formats/#profiles
- Somehow we need to detect the color system being used by the input file and handle each case differently (with profiles)
- This is trivial with `identify` (even by the Java ImageMagick API):

    $ identify -format '%r\n' alc_contrastes_desafios.pdf\[0\]
    DirectClass CMYK
    $ identify -format '%r\n' Africa\ group\ of\ negotiators.pdf\[0\]
    DirectClass sRGB Alpha

## 2017-03-04

- Spent more time looking at the ImageMagick CMYK issue
- The `default_cmyk.icc` and `default_rgb.icc` files are both part of the Ghostscript GPL distribution, but according to DSpace’s `LICENSES_THIRD_PARTY` file, DSpace doesn’t allow distribution of dependencies that are licensed solely under the GPL
- So this issue is kinda pointless now, as the ICC profiles are absolutely necessary to make a meaningful CMYK→sRGB conversion

## 2017-03-05

- Look into helping developers from landportal.info with a query for items related to LAND on the REST API
- They want something like the items that are returned by the general “LAND” query in the search interface, but we cannot do that
- We can only return specific results for metadata fields, like:

    $ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "LAND REFORM", "language": null}' | json_pp

- But there are hundreds of combinations of fields and values (like `dc.subject` and all the center subjects), and we can’t use wildcards in REST!
- Reading about enabling multiple handle prefixes in DSpace
- There is a mailing list thread from 2011 about it: http://dspace.2283337.n4.nabble.com/Multiple-handle-prefixes-merged-DSpace-instances-td3427192.html
- And a comment from Atmire’s Bram about it on the DSpace wiki: https://wiki.lyrasis.org/display/DSDOC5x/Installing+DSpace?focusedCommentId=78163296#comment-78163296
- Bram mentions an undocumented configuration option `handle.plugin.checknameauthority`, but I noticed another one in `dspace.cfg`:

    # List any additional prefixes that need to be managed by this handle server
    # (as for examle handle prefix coming from old dspace repository merged in
    # that repository)
    # handle.additional.prefixes = prefix1[, prefix2]

- Because of this I noticed that our Handle server’s `config.dct` was potentially misconfigured!
- We had some default values still present:

    "300:0.NA/YOUR_NAMING_AUTHORITY"

- I’ve changed them to the following and restarted the handle server:

    "300:0.NA/10568"

- In looking at all the configs I just noticed that we are not providing a DOI in the Google-specific metadata crosswalk
- From `dspace/config/crosswalks/google-metadata.properties`:

    google.citation_doi = cg.identifier.doi

- This works, and makes DSpace output the following metadata on the item view page:

    <meta content="https://dx.doi.org/10.1186/s13059-017-1153-y" name="citation_doi">

- Submitted and merged pull request for this: https://github.com/ilri/DSpace/pull/305
- Submit pull request to set the author separator for XMLUI item lists to a semicolon instead of “,": https://github.com/ilri/DSpace/pull/306
- I want to show it briefly to Abenet and Peter to get feedback

## 2017-03-06

- Someone on the mailing list said that `handle.plugin.checknameauthority` should be false if we’re using multiple handle prefixes

## 2017-03-07

- I set up a top-level community as a test for the CGIAR Library and imported one item with the the 10947 handle prefix
- When testing the Handle resolver locally it shows the item to be on the local repository
- So this seems to work, with the following caveats:
  - New items will have the default handle
  - Communities and collections will have the default handle
  - Only items imported manually can have the other handles
- I need to talk to Michael and Peter to share the news, and discuss the structure of their community(s) and try some actual test data
- We’ll need to do some data cleaning to make sure they are using the same fields we are, like `dc.type` and `cg.identifier.status`
- Another thing is that the import process creates new `dc.date.accessioned` and `dc.date.available` fields, so we end up with duplicates (is it important to preserve the originals for these?)
- Report DS-3520 issue to Atmire

## 2017-03-08

- Merge the author separator changes to `5_x-prod`, as everyone has responded positively about it, and it’s the default in Mirage2 afterall!
- Cherry pick the `commons-collections` patch from DSpace’s `dspace-5_x` branch to address DS-3520: https://jira.duraspace.org/browse/DS-3520

## 2017-03-09

- Export list of sponsors so Peter can clean it up:

    dspace=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'description' and qualifier = 'sponsorship') group by text_value order by count desc) to /tmp/sponsorship.csv with csv;
    COPY 285

## 2017-03-12

- Test the sponsorship fixes and deletes from Peter:

    $ ./fix-metadata-values.py -i Investors-Fix-51.csv -f dc.description.sponsorship -t Action -m 29 -d dspace -u dspace -p fuuuu
    $ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.sponsorship -m 29 -d dspace -u dspace -p fuuu

- Generate a new list of unique sponsors so we can update the controlled vocabulary:

    dspace=# \copy (select distinct text_value from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'description' and qualifier = 'sponsorship')) to /tmp/sponsorship.csv with csv;

- Pull request for controlled vocabulary if Peter approves: https://github.com/ilri/DSpace/pull/308
- Review Sisay’s roots, tubers, and bananas (RTB) theme, which still needs some fixes to work properly: https://github.com/ilri/DSpace/pull/307
- Created an issue to track the progress on the Livestock CRP theme: https://github.com/ilri/DSpace/issues/309
- Created a basic theme for the Livestock CRP community

## 2017-03-15

- Merge pull request for controlled vocabulary updates for sponsor: https://github.com/ilri/DSpace/pull/308
- Merge pull request for Livestock CRP theme: https://github.com/ilri/DSpace/issues/309
- Create pull request for PABRA subjects (waiting for confirmation from Abenet before merging): https://github.com/ilri/DSpace/pull/310
- Create pull request for CCAFS Phase II migrations (waiting for confirmation from CCAFS people): https://github.com/ilri/DSpace/pull/311
- I also need to ask if either of these new fields need to be added to Discovery facets, search, and Atmire modules
- Run all system updates on DSpace Test and re-deploy CGSpace

## 2017-03-16

- Merge pull request for PABRA subjects: https://github.com/ilri/DSpace/pull/310
- Abenet and Peter say we can add them to Discovery, Atmire modules, etc, but I might not have time to do it now
- Help Sisay with RTB theme again
- Remove ICARDA subject from Discovery sidebar facets: https://github.com/ilri/DSpace/pull/312
- Remove ICARDA subject from Browse and item submission form: https://github.com/ilri/DSpace/pull/313
- Merge the CCAFS Phase II changes but hold off on doing the flagship metadata updates until Macaroni Bros gets their importer updated
- Deploy latest changes and investor fixes/deletions on CGSpace
- Run system updates on CGSpace and reboot server

## 2017-03-20

- Create basic XMLUI theme for PABRA community: https://github.com/ilri/DSpace/pull/315

## 2017-03-24

- Still helping Sisay try to figure out how to create a theme for the RTB community

## 2017-03-28

- CCAFS said they are ready for the flagship updates for Phase II to be run (`cg.subject.ccafs`), so I ran them on CGSpace:

    $ ./fix-metadata-values.py -i ccafs-flagships-feb7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu

- We’ve been waiting since February to run these
- Also, I generated a list of all CCAFS flagships because there are a dozen or so more than there should be:

    dspace=# \copy (select distinct text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=210 group by text_value order by count desc) to /tmp/ccafs.csv with csv;

- I sent a list to CCAFS people so they can tell me if some should be deleted or moved, etc
- Test, squash, and merge Sisay’s RTB theme into `5_x-prod`: https://github.com/ilri/DSpace/pull/316

## 2017-03-29

- Dump a list of fields in the DC and CG schemas to compare with CG Core:

    dspace=# select case when metadata_schema_id=1 then 'dc' else 'cg' end as schema, element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id in (1, 2);

- Ooh, a better one!

    dspace=# select coalesce(case when metadata_schema_id=1 then 'dc.' else 'cg.' end) || concat_ws('.', element, qualifier) as field, scope_note from metadatafieldregistry where metadata_schema_id in (1, 2);

## 2017-03-30

- Adjust the Linode CPU usage alerts for the CGSpace server from 150% to 200%, as generally the nightly Solr indexing causes a usage around 150–190%, so this should make the alerts less regular
- Adjust the threshold for DSpace Test from 90 to 100%