--- title: "September, 2023" date: 2023-09-02T17:29:36+03:00 author: "Alan Orth" categories: ["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](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 - 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: ```console $ 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: ```console $ ./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: ```console $ 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](https://www.altmetric.com/explorer/documentation/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 - 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: ```console $ 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](https://unix.stackexchange.com/questions/274548/join-two-files-each-with-two-columns-including-non-matching-lines): ```console $ 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: ```json { "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](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 ## 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