September, 2023
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…
- It still feels hacky, but using AfterViewInit, and importing the Altmetric
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
andprepress
presets:
- I used GhostScript to try reducing it using the
$ 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
- Also, he said he had to reduce
- 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 ofhref
when I am constructing links- The
routerLink
routes within the single page application and saves state, while thehref
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
- The
2023-09-17
- I added an About page to DSpace 7 Test using similar logic to the privacy page
2023-09-18
- 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
- I filed a GitHub issue for the search filters capitalizing metadata values: https://github.com/DSpace/dspace-angular/issues/2501
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
- First I exported CGSpace and extracted the
- 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 satisfyjoin
- 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