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238 lines
12 KiB
Markdown
238 lines
12 KiB
Markdown
+++
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date = "2017-03-01T17:08:52+02:00"
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author = "Alan Orth"
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title = "March, 2017"
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tags = ["Notes"]
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+++
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## 2017-03-01
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- Run the 279 CIAT author corrections on CGSpace
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## 2017-03-02
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- Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
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- CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
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- They might come in at the top level in one "CGIAR System" community, or with several communities
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- 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?
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- Need to send Peter and Michael some notes about this in a few days
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- Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
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- 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](https://jira.duraspace.org/browse/DS-3516)
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- Discovered that the ImageMagic `filter-media` plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
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- 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](https://cgspace.cgiar.org/handle/10568/51999)):
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```
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$ identify ~/Desktop/alc_contrastes_desafios.jpg
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/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
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```
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<!--more-->
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- This results in discolored thumbnails when compared to the original PDF, for example sRGB and CMYK:
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- I filed an issue for the color space thing: [DS-3517](https://jira.duraspace.org/browse/DS-3517)
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## 2017-03-03
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- I created a patch for DS-3517 and made a pull request against upstream `dspace-5_x`: https://github.com/DSpace/DSpace/pull/1669
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- Looks like `-colorspace sRGB` alone isn't enough, we need to use profiles:
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```
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$ 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
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```
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- This reads the input file, applies the CMYK profile, applies the RGB profile, then writes the file
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- Note that you should set the first profile immediately after the input file
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- Also, it is better to use profiles than setting `-colorspace`
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- This is a great resource describing the color stuff: http://www.imagemagick.org/Usage/formats/#profiles
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- Somehow we need to detect the color system being used by the input file and handle each case differently (with profiles)
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- This is trivial with `identify` (even by the [Java ImageMagick API](http://im4java.sourceforge.net/api/org/im4java/core/IMOps.html#identify)):
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```
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$ identify -format '%r\n' alc_contrastes_desafios.pdf\[0\]
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DirectClass CMYK
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$ identify -format '%r\n' Africa\ group\ of\ negotiators.pdf\[0\]
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DirectClass sRGB Alpha
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```
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## 2017-03-04
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- Spent more time looking at the ImageMagick CMYK issue
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- 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
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- So this issue is kinda pointless now, as the ICC profiles are absolutely necessary to make a meaningful CMYK→sRGB conversion
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## 2017-03-05
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- Look into helping developers from landportal.info with a query for items related to LAND on the REST API
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- They want something like the items that are returned by the general "LAND" query in the search interface, but we cannot do that
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- We can only return specific results for metadata fields, like:
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```
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$ 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
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```
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- 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!
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- Reading about enabling multiple handle prefixes in DSpace
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- There is a mailing list thread from 2011 about it: http://dspace.2283337.n4.nabble.com/Multiple-handle-prefixes-merged-DSpace-instances-td3427192.html
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- 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
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- Bram mentions an undocumented configuration option `handle.plugin.checknameauthority`, but I noticed another one in `dspace.cfg`:
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```
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# List any additional prefixes that need to be managed by this handle server
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# (as for examle handle prefix coming from old dspace repository merged in
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# that repository)
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# handle.additional.prefixes = prefix1[, prefix2]
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```
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- Because of this I noticed that our Handle server's `config.dct` was potentially misconfigured!
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- We had some default values still present:
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```
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"300:0.NA/YOUR_NAMING_AUTHORITY"
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```
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- I've changed them to the following and restarted the handle server:
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```
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"300:0.NA/10568"
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```
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- In looking at all the configs I just noticed that we are not providing a DOI in the Google-specific metadata crosswalk
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- From `dspace/config/crosswalks/google-metadata.properties`:
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```
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google.citation_doi = cg.identifier.doi
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```
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- This works, and makes DSpace output the following metadata on the item view page:
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```
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<meta content="https://dx.doi.org/10.1186/s13059-017-1153-y" name="citation_doi">
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```
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- Submitted and merged pull request for this: https://github.com/ilri/DSpace/pull/305
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- Submit pull request to set the author separator for XMLUI item lists to a semicolon instead of ",": https://github.com/ilri/DSpace/pull/306
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- I want to show it briefly to Abenet and Peter to get feedback
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## 2017-03-06
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- Someone on the mailing list said that `handle.plugin.checknameauthority` should be false if we're using multiple handle prefixes
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## 2017-03-07
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- I set up a top-level community as a test for the CGIAR Library and imported one item with the the 10947 handle prefix
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- When testing the Handle resolver locally it shows the item to be on the local repository
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- So this seems to work, with the following caveats:
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- New items will have the default handle
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- Communities and collections will have the default handle
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- Only items imported manually can have the other handles
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- 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
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- 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`
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- 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?)
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- Report DS-3520 issue to Atmire
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## 2017-03-08
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- Merge the author separator changes to `5_x-prod`, as everyone has responded positively about it, and it's the default in Mirage2 afterall!
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- Cherry pick the `commons-collections` patch from DSpace's `dspace-5_x` branch to address DS-3520: https://jira.duraspace.org/browse/DS-3520
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## 2017-03-09
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- Export list of sponsors so Peter can clean it up:
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```
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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;
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COPY 285
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```
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## 2017-03-12
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- Test the sponsorship fixes and deletes from Peter:
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```
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$ ./fix-metadata-values.py -i Investors-Fix-51.csv -f dc.description.sponsorship -t Action -m 29 -d dspace -u dspace -p fuuuu
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$ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.sponsorship -m 29 -d dspace -u dspace -p fuuu
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```
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- Generate a new list of unique sponsors so we can update the controlled vocabulary:
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```
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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;
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```
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- Pull request for controlled vocabulary if Peter approves: https://github.com/ilri/DSpace/pull/308
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- Review Sisay's roots, tubers, and bananas (RTB) theme, which still needs some fixes to work properly: https://github.com/ilri/DSpace/pull/307
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- Created an issue to track the progress on the Livestock CRP theme: https://github.com/ilri/DSpace/issues/309
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- Created a basic theme for the Livestock CRP community
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## 2017-03-15
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- Merge pull request for controlled vocabulary updates for sponsor: https://github.com/ilri/DSpace/pull/308
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- Merge pull request for Livestock CRP theme: https://github.com/ilri/DSpace/issues/309
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- Create pull request for PABRA subjects (waiting for confirmation from Abenet before merging): https://github.com/ilri/DSpace/pull/310
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- Create pull request for CCAFS Phase II migrations (waiting for confirmation from CCAFS people): https://github.com/ilri/DSpace/pull/311
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- I also need to ask if either of these new fields need to be added to Discovery facets, search, and Atmire modules
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- Run all system updates on DSpace Test and re-deploy CGSpace
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## 2017-03-16
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- Merge pull request for PABRA subjects: https://github.com/ilri/DSpace/pull/310
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- Abenet and Peter say we can add them to Discovery, Atmire modules, etc, but I might not have time to do it now
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- Help Sisay with RTB theme again
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- Remove ICARDA subject from Discovery sidebar facets: https://github.com/ilri/DSpace/pull/312
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- Remove ICARDA subject from Browse and item submission form: https://github.com/ilri/DSpace/pull/313
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- Merge the CCAFS Phase II changes but hold off on doing the flagship metadata updates until Macaroni Bros gets their importer updated
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- Deploy latest changes and investor fixes/deletions on CGSpace
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- Run system updates on CGSpace and reboot server
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## 2017-03-20
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- Create basic XMLUI theme for PABRA community: https://github.com/ilri/DSpace/pull/315
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## 2017-03-24
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- Still helping Sisay try to figure out how to create a theme for the RTB community
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## 2017-03-28
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- CCAFS said they are ready for the flagship updates for Phase II to be run (`cg.subject.ccafs`), so I ran them on CGSpace:
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```
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$ ./fix-metadata-values.py -i ccafs-flagships-feb7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu
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```
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- We've been waiting since February to run these
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- Also, I generated a list of all CCAFS flagships because there are a dozen or so more than there should be:
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```
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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;
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```
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- I sent a list to CCAFS people so they can tell me if some should be deleted or moved, etc
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- Test, squash, and merge Sisay's RTB theme into `5_x-prod`: https://github.com/ilri/DSpace/pull/316
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## 2017-03-29
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- Dump a list of fields in the DC and CG schemas to compare with CG Core:
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```
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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);
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```
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- Ooh, a better one!
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```
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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);
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```
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## 2017-03-30
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- 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
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- Adjust the threshold for DSpace Test from 90 to 100%
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