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244 lines
12 KiB
Markdown
244 lines
12 KiB
Markdown
---
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title: "September, 2023"
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date: 2023-09-02T17:29:36+03:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2023-09-02
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- Export CGSpace to check for missing Initiative collection mappings
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- Start a harvest on AReS
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<!--more-->
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## 2023-09-03
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- I figured out how to use Altmetric and Dimensions badges in the DSpace Angular frontend
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- It still feels hacky, but using [AfterViewInit](https://stackoverflow.com/questions/41936631/how-to-trigger-the-function-after-dom-markup-is-loaded-in-angular-style-applicat), and importing the Altmetric `embed.js` in the component works
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- The style on mobile also needs work...
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## 2023-09-06
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- Discussion with Marie about finalizing the output types list on GitHub
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- I did some review and cleanup in preparation for publishing the new list
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## 2023-09-07
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- Export CGSpace to start doing a review of the metadata
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- First I will start by extracting all items with DOIs, along with some fields I can compare against Crossref:
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```console
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$ csvgrep -c 'cg.identifier.doi[en_US]' -r 'doi.org' ~/Downloads/2023-09-07-cgspace.csv \
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| csvcut -c 'id,dc.title[en_US],dcterms.issued[en_US],dcterms.available[en_US],cg.issn[en_US],cg.isbn[en_US],cg.volume[en_US],cg.issue[en_US],cg.number[en_US],dcterms.extent[en_US],cg.identifier.doi[en_US],cg.reviewStatus[en_US],cg.isijournal[en_US],dcterms.license[en_US],dcterms.accessRights[en_US],dcterms.type[en_US],dc.identifier.uri[en_US]' \
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> /tmp/2023-09-07-cgspace-dois.csv
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$ csvgrep -c 'cg.identifier.doi[en_US]' -r 'doi.org' ~/Downloads/2023-09-07-cgspace.csv | csvcut -c 'cg.identifier.doi[en_US]' | sed 1d > /tmp/2023-09-07-cgspace-dois.txt
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```
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- Then I resolved the DOIs from Crossref:
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```console
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$ ./ilri/crossref_doi_lookup.py -i /tmp/2023-09-07-cgspace-dois.txt -o /tmp/2023-09-07-cgspace-dois-results.csv -e a.orth@cgiar.org
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```
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- A user emailed to ask about uploading a 180MB PDF to CGSpace
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- I used GhostScript to try reducing it using the `screen`, `ebook` and `prepress` presets:
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```console
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$ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile=primer-screen.pdf Primer\ \(digital\)_Climate-\ smart\ and\ regenerative\ agriculture\ in\ climate\ change\ adaptation.pdf
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$ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -dQUIET -dBATCH -sOutputFile=primer-ebook.pdf Primer\ \(digital\)_Climate-\ smart\ and\ regenerative\ agriculture\ in\ climate\ change\ adaptation.pdf
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$ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/prepress -dNOPAUSE -dQUIET -dBATCH -sOutputFile=primer-prepress.pdf Primer\ \(digital\)_Climate-\ smart\ and\ regenerative\ agriculture\ in\ climate\ change\ adaptation.pdf
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```
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- The `prepress` one is 300DPI and looks visually identical to the original, so I proposed that we use that one
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## 2023-09-08
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- I did a review of the metadata for our items with DOIs, comparing with data from Crossref
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- I spot checked a handful of issue / online dates and licenses, and saw that Crossref's dates are always more accurate than ours when they differ
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- I also filled in some missing volumes, issues, ISSNs, and extents
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- This results in 14,000 changes to existing items, which will take several days to import unfortunately
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- After eight hours the first file is only about 2/3 finished... sigh
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- Meet with Peter to discuss changes to the DSpace 7 test
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- Minor updates to submission forms and some new ideas for the home page and item page
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- I figured out how to use a themed home page component and add a cards UI to our CGSpace theme
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## 2023-09-09
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- I can't believe that almost 18 hours later the first CSV import with 5,000 changes is not done...
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- Run all system updates on CGSpace and reboot it, as it had been two months since the last time
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## 2023-09-10
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- Minor work on the DSpace 7 home page
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## 2023-09-11
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- Export CGSpace to check for missing Initiative collection mappings
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- Start a harvest on AReS
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## 2023-09-12
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- Minor work on DSpace 7 home page
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- Minor work on CG Core types
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- I published a new HTML version of the updated IPtypes and archived the current version as v2.0.0 so we can still reference it
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## 2023-09-13
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- Stefano reminded me about the updated OAI MODS mappings on CGSpace so I re-applied them on DSpace Test and updated the OAI index so he could confirm
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- Now I'm ready to put it on CGSpace if he confirms
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- I created a basic theme for CIP on DSpace 7
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- While doing that I noticed that a bunch of CIP bitstreams didn't have the latest 500px thumbnails so I re-ran filter-media on a handful of their collections
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- I had two occurrences of an OOM kill of the Tomcat 9 java process on DSpace 7 test tonight
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- Once while doing a Discovery index, the other while doing filter media
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## 2023-09-15
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- Discuss issues with the Altmetric API with the Altmetric support team
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- Apparently we can use a different API, the [Explorer API](https://www.altmetric.com/explorer/documentation/api), since we already have access to the Explorer dashboard
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- I reduced the Solr heap size on DSpace 7 from 3GB to 2GB
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- Apparentlty I already did this from 4GB to 3GB a few months ago
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- The Solr admin interface was showing Solr taking ~1GB of RAM so I think this should be safe
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- Mark on DSpace Slack said he uses PM2's `--max-memory-restart` so the processes restart when they hit the limit
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- Also, he said he had to reduce `cache:serverSide:botCache:max` from 1000 to 500 to cache less SSR pages in memory
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- I decided to try deploying DSpace 7 Test on a Hetzner server with 64GB RAM, 6 CPUs, and 2x512GB NVMe SSD
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## 2023-09-16
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- Export CGSpace to check for missing Initiative collection mappings
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- Start a harvest on AReS
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- Configure the privacy policy page on DSpace 7 using a themed component with the text from our DSpace 6 site
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- I realized that for all my custom Angular components I should be using `routerLink` instead of `href` when I am constructing links
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- The `routerLink` routes within the single page application and saves state, while the `href` reloads the page
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- Using the `routerLink` way is faster and results in less flashing and jumping in the page when navigating
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- See: https://stackoverflow.com/a/61588147
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## 2023-09-17
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- I added an About page to DSpace 7 Test using similar logic to the privacy page
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## 2023-09-18
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- I filed a GitHub issue for being unable to navigate dropdown lists using the keyboard on the dspace-angular submission form: https://github.com/DSpace/dspace-angular/issues/2500
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- I filed a GitHub issue for the search filters capitalizing metadata values: https://github.com/DSpace/dspace-angular/issues/2501
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## 2023-09-19
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- Complete migration of DSpace 7 Test from Linode to Hetzner
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- Export some years of Solr stats from CGSpace to import on the new DSpace 7 Test:
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```console
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$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/statistics-2020-2022.json -f 'time:[2020-01-01T00\:00\:00Z TO 2022-12-31T23\:59\:59Z]' -k uid -S actingGroupId,actingGroupParentId,actorMemberGroupId,author_mtdt,author_mtdt_search,bitstreamCount,bitstreamId,complete_query,complete_query_search,containerBitstream,containerCollection,containerCommunity,containerItem,core_update_run_nb,countryCode_ngram,countryCode_search,cua_version,dateYear,dateYearMonth,file_id,filterquery,first_name,geoipcountrycode,geoIpCountryCode,group_id,group_map,group_name,ip_ngram,ip_search,isArchived,isInternal,iso_mtdt,iso_mtdt_search,isWithdrawn,last_name,name,ngram_query_search,ngram_simplequery_search,orphaned,parent_count,p_communities_id,p_communities_map,p_communities_name,p_group_id,p_group_map,p_group_name,range,rangeDescription,rangeDescription_ngram,rangeDescription_search,range_ngram,range_search,referrer_ngram,referrer_search,simple_query,simple_query_search,solr_update_time_stamp,storage_nb_of_bitstreams,storage_size,storage_statistics_type,subject_mtdt,subject_mtdt_search,text,userAgent_ngram,userAgent_search,version_id,workflowItemId
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```
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- Ben sent me an export of ILRI presentations from Slideshare and asked if we could see if any are missing on CGSpace
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- First I exported CGSpace and extracted the `cg.identifier.url` column so I could normalize all Slideshare URLs to use "https://www.slideshare.net" instead of localized variants (es.slideshare.net, fr.slideshare.net, etc) as well as non-https links and links with query params and slashes at the end
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- This was about 250 URLs
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- I extracted the URL field from both our list and the Slideshare list and then used [GNU `join` to print non-matched lines](https://unix.stackexchange.com/questions/274548/join-two-files-each-with-two-columns-including-non-matching-lines):
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```console
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$ join -t, -v 2 -11 -21 -o auto /tmp/cgspace-ilri-slideshare-sorted-only-urls-sorted.csv /tmp/ilri-slideshare-sorted-sorted.csv | wc -l
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542
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```
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- Important to note that you must use GNU `sort` on the fiels first, as I had tried sorting in vim and it didn't satisfy `join`
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- So it seems there are 542 Slideshare presentations we are missing
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## 2023-09-20
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- Regarding the incorrect city in Solr statistics, I see we have 1,600,000 of them
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- Before filing a GitHub issue, I want to check if they maybe come from an Atmire module, as I see them clustered around two particular CUA versions:
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```json
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{
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"responseHeader": {
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"status": 0,
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"QTime": 2760,
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"params": {
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"q": "city:com.maxmind.geoip2.record.City*",
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"facet.field": "cua_version",
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"indent": "true",
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"rows": "0",
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"wt": "json",
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"facet": "true",
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"_": "1695192301927"
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}
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},
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"response": {
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"numFound": 1661863,
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"start": 0,
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"docs": []
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},
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"facet_counts": {
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"facet_queries": {},
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"facet_fields": {
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"cua_version": [
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"6.x-4.1.10-ilri-RC7",
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1112186,
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"6.x-4.1.10-ilri-RC5",
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451180,
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"6.x-4.1.10-ilri-RC9",
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0
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]
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},
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"facet_dates": {},
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"facet_ranges": {},
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"facet_intervals": {}
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}
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}
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```
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- I migrated AReS from Linode to Hetzner
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- I asked on Slack and someone told me that we need to edit `src/app/menu.resolver.ts` to add new drop down menus to the top navbar
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- It works, though is unfortunate that we can't do it in a theme
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## 2023-09-21
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- More minor work on DSpace 7 home page and menus
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- Meeting to discuss types and DSpace 7 migration plans
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- Create a DSpace 7 theme for IITA
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## 2023-09-22
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- Create a DSpace 7 theme for IWMI
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- I had some issues with pm2 on the new DSpace 7 Test
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- It seems to be due to mixing systemd starting versus manually starting / stopping...
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- After reading the discussion in [this pm2 issue](https://github.com/Unitech/pm2/issues/2914) I realize that we probably need to use `--no-daemon` to have systemd fully manage the processes without pm2 trying to save state
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## 2023-09-23
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- Export CGSpace to check for missing Initiative collection mappings
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- Start a harvest on AReS
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## 2023-09-25
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- CGSpace metadata and community / collection cleanup
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- Review some patches on DSpace Angular
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- Create a basic Alliance theme for DSpace 7
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## 2023-09-27
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- I realized that we can get controlled vocabularies from DSpace 7's REST API, for both value-pairs and hierarchical controlled vocabularies, ie:
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https://dspace7test.ilri.org/server/api/submission/vocabularies/common_iso_languages/entries
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## 2023-09-29
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- Meeting with Aditi and others to discuss plan for using CGSpace to do a systematic review of CGIAR research on climate change
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- I cleaned up metadata for a hundred or so items, and realized we will need to do more to make sure abstracts and open access status are correct since there will be a laser focus on the metadata
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## 2023-09-30
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- Export CGSpace to check for missing Initiative collection mappings
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- Still working on checking Unpaywall for access rights and licenses for our DOIs
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- Regarding Unpaywall's "evidence" metadata about whether an item is open access or not, after looking at dozens of items manually:
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- evidence: "oa journal (via doaj)" <---- yes
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- evidence: "open (via free article)" <---- hmmm, not always correct
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- evidence: "open (via page says license)" <--- noooo, can't rely on that
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- evidence: "open (via page says Open Access)" <---- yes...?
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- evidence: "open (via free pdf)" <---- hmmm, not always correct
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- evidence: "oa journal (via publisher name)" <---- noooo
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- I updated access status for about four hundred more items based on this, and licenses for a dozen or so
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<!-- vim: set sw=2 ts=2: -->
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