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cgspace-notes/content/posts/2023-09.md
Alan Orth cb40610726
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2023-10-04 09:24:33 +03:00

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September, 2023 2023-09-02T17:29:36+03:00 Alan Orth
Notes

2023-09-02

  • Export CGSpace to check for missing Initiative collection mappings
  • Start a harvest on AReS

2023-09-03

  • I figured out how to use Altmetric and Dimensions badges in the DSpace Angular frontend
    • It still feels hacky, but using AfterViewInit, and importing the Altmetric embed.js in the component works
    • The style on mobile also needs work...

2023-09-06

  • Discussion with Marie about finalizing the output types list on GitHub
    • I did some review and cleanup in preparation for publishing the new list

2023-09-07

  • Export CGSpace to start doing a review of the metadata
  • First I will start by extracting all items with DOIs, along with some fields I can compare against Crossref:
$ csvgrep -c 'cg.identifier.doi[en_US]' -r 'doi.org' ~/Downloads/2023-09-07-cgspace.csv \
    | 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]' \
    > /tmp/2023-09-07-cgspace-dois.csv
$ 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
  • Then I resolved the DOIs from Crossref:
$ ./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
  • A user emailed to ask about uploading a 180MB PDF to CGSpace
    • I used GhostScript to try reducing it using the screen, ebook and prepress presets:
$ 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 
$ 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
$ 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
  • The prepress one is 300DPI and looks visually identical to the original, so I proposed that we use that one

2023-09-08

  • I did a review of the metadata for our items with DOIs, comparing with data from Crossref
    • 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
    • I also filled in some missing volumes, issues, ISSNs, and extents
    • This results in 14,000 changes to existing items, which will take several days to import unfortunately
    • After eight hours the first file is only about 2/3 finished... sigh
  • Meet with Peter to discuss changes to the DSpace 7 test
    • Minor updates to submission forms and some new ideas for the home page and item page
  • I figured out how to use a themed home page component and add a cards UI to our CGSpace theme

2023-09-09

  • I can't believe that almost 18 hours later the first CSV import with 5,000 changes is not done...
  • Run all system updates on CGSpace and reboot it, as it had been two months since the last time

2023-09-10

  • Minor work on the DSpace 7 home page

2023-09-11

  • Export CGSpace to check for missing Initiative collection mappings
  • Start a harvest on AReS

2023-09-12

  • Minor work on DSpace 7 home page
  • Minor work on CG Core types
    • 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

2023-09-13

  • 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
    • Now I'm ready to put it on CGSpace if he confirms
  • I created a basic theme for CIP on DSpace 7
    • 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
  • I had two occurrences of an OOM kill of the Tomcat 9 java process on DSpace 7 test tonight
    • Once while doing a Discovery index, the other while doing filter media

2023-09-15

  • Discuss issues with the Altmetric API with the Altmetric support team
    • Apparently we can use a different API, the Explorer API, since we already have access to the Explorer dashboard
  • I reduced the Solr heap size on DSpace 7 from 3GB to 2GB
    • Apparentlty I already did this from 4GB to 3GB a few months ago
    • The Solr admin interface was showing Solr taking ~1GB of RAM so I think this should be safe
  • Mark on DSpace Slack said he uses PM2's --max-memory-restart so the processes restart when they hit the limit
    • Also, he said he had to reduce cache:serverSide:botCache:max from 1000 to 500 to cache less SSR pages in memory
  • I decided to try deploying DSpace 7 Test on a Hetzner server with 64GB RAM, 6 CPUs, and 2x512GB NVMe SSD

2023-09-16

  • Export CGSpace to check for missing Initiative collection mappings
  • Start a harvest on AReS
  • Configure the privacy policy page on DSpace 7 using a themed component with the text from our DSpace 6 site
  • I realized that for all my custom Angular components I should be using routerLink instead of href when I am constructing links
    • The routerLink routes within the single page application and saves state, while the href reloads the page
    • Using the routerLink way is faster and results in less flashing and jumping in the page when navigating
    • See: https://stackoverflow.com/a/61588147

2023-09-17

  • I added an About page to DSpace 7 Test using similar logic to the privacy page

2023-09-18

2023-09-19

  • Complete migration of DSpace 7 Test from Linode to Hetzner
  • Export some years of Solr stats from CGSpace to import on the new DSpace 7 Test:
$ 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
  • Ben sent me an export of ILRI presentations from Slideshare and asked if we could see if any are missing on CGSpace
    • 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
    • This was about 250 URLs
  • I extracted the URL field from both our list and the Slideshare list and then used GNU join to print non-matched lines:
$ 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
542
  • 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
  • So it seems there are 542 Slideshare presentations we are missing

2023-09-20

  • Regarding the incorrect city in Solr statistics, I see we have 1,600,000 of them
    • 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:
{
  "responseHeader": {
    "status": 0,
    "QTime": 2760,
    "params": {
      "q": "city:com.maxmind.geoip2.record.City*",
      "facet.field": "cua_version",
      "indent": "true",
      "rows": "0",
      "wt": "json",
      "facet": "true",
      "_": "1695192301927"
    }
  },
  "response": {
    "numFound": 1661863,
    "start": 0,
    "docs": []
  },
  "facet_counts": {
    "facet_queries": {},
    "facet_fields": {
      "cua_version": [
        "6.x-4.1.10-ilri-RC7",
        1112186,
        "6.x-4.1.10-ilri-RC5",
        451180,
        "6.x-4.1.10-ilri-RC9",
        0
      ]
    },
    "facet_dates": {},
    "facet_ranges": {},
    "facet_intervals": {}
  }
}
  • I migrated AReS from Linode to Hetzner
  • 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
    • It works, though is unfortunate that we can't do it in a theme

2023-09-21

  • More minor work on DSpace 7 home page and menus
  • Meeting to discuss types and DSpace 7 migration plans
  • Create a DSpace 7 theme for IITA

2023-09-22

  • Create a DSpace 7 theme for IWMI
  • I had some issues with pm2 on the new DSpace 7 Test
    • It seems to be due to mixing systemd starting versus manually starting / stopping...
    • After reading the discussion in this pm2 issue I realize that we probably need to use --no-daemon to have systemd fully manage the processes without pm2 trying to save state

2023-09-23

  • Export CGSpace to check for missing Initiative collection mappings
  • Start a harvest on AReS

2023-09-25

  • CGSpace metadata and community / collection cleanup
  • Review some patches on DSpace Angular
  • Create a basic Alliance theme for DSpace 7

2023-09-27

  • I realized that we can get controlled vocabularies from DSpace 7's REST API, for both value-pairs and hierarchical controlled vocabularies, ie:

https://dspace7test.ilri.org/server/api/submission/vocabularies/common_iso_languages/entries

2023-09-29

  • Meeting with Aditi and others to discuss plan for using CGSpace to do a systematic review of CGIAR research on climate change
  • 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

2023-09-30

  • Export CGSpace to check for missing Initiative collection mappings
  • Still working on checking Unpaywall for access rights and licenses for our DOIs
  • Regarding Unpaywall's "evidence" metadata about whether an item is open access or not, after looking at dozens of items manually:
    • evidence: "oa journal (via doaj)" <---- yes
    • evidence: "open (via free article)" <---- hmmm, not always correct
    • evidence: "open (via page says license)" <--- noooo, can't rely on that
    • evidence: "open (via page says Open Access)" <---- yes...?
    • evidence: "open (via free pdf)" <---- hmmm, not always correct
    • evidence: "oa journal (via publisher name)" <---- noooo
  • I updated access status for about four hundred more items based on this, and licenses for a dozen or so