From 2d8532e10e736ecc5c9196de9557179b6a0e8631 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Wed, 3 Aug 2022 21:01:39 +0300 Subject: [PATCH] Add notes for 2022-08-03 --- content/posts/2022-06.md | 2 +- content/posts/2022-08.md | 52 +++++++++++++++++ docs/2015-11/index.html | 2 +- docs/2015-12/index.html | 2 +- docs/2016-01/index.html | 2 +- docs/2016-02/index.html | 2 +- docs/2016-03/index.html | 2 +- docs/2016-04/index.html | 2 +- docs/2016-05/index.html | 2 +- docs/2016-06/index.html | 2 +- docs/2016-07/index.html | 2 +- docs/2016-08/index.html | 2 +- docs/2016-09/index.html | 2 +- docs/2016-10/index.html | 2 +- docs/2016-11/index.html | 2 +- docs/2016-12/index.html | 2 +- docs/2017-01/index.html | 2 +- docs/2017-02/index.html | 2 +- docs/2017-03/index.html | 2 +- docs/2017-04/index.html | 2 +- docs/2017-05/index.html | 2 +- docs/2017-06/index.html | 2 +- docs/2017-07/index.html | 2 +- docs/2017-08/index.html | 2 +- docs/2017-09/index.html | 2 +- docs/2017-10/index.html | 2 +- docs/2017-11/index.html | 2 +- docs/2017-12/index.html | 2 +- docs/2018-01/index.html | 2 +- docs/2018-02/index.html | 2 +- docs/2018-03/index.html | 2 +- docs/2018-04/index.html | 2 +- docs/2018-05/index.html | 2 +- docs/2018-06/index.html | 2 +- docs/2018-07/index.html | 2 +- docs/2018-08/index.html | 2 +- docs/2018-09/index.html | 2 +- docs/2018-10/index.html | 2 +- docs/2018-11/index.html | 2 +- docs/2018-12/index.html | 2 +- docs/2019-01/index.html | 2 +- docs/2019-02/index.html | 2 +- docs/2019-03/index.html | 2 +- docs/2019-04/index.html | 2 +- docs/2019-05/index.html | 2 +- docs/2019-06/index.html | 2 +- docs/2019-07/index.html | 2 +- docs/2019-08/index.html | 2 +- docs/2019-09/index.html | 2 +- docs/2019-10/index.html | 2 +- docs/2019-11/index.html | 2 +- docs/2019-12/index.html | 2 +- docs/2020-01/index.html | 2 +- docs/2020-02/index.html | 2 +- docs/2020-03/index.html | 2 +- docs/2020-04/index.html | 2 +- docs/2020-05/index.html | 2 +- docs/2020-06/index.html | 2 +- docs/2020-07/index.html | 2 +- docs/2020-08/index.html | 2 +- docs/2020-09/index.html | 2 +- docs/2020-10/index.html | 2 +- docs/2020-11/index.html | 2 +- docs/2020-12/index.html | 2 +- docs/2021-01/index.html | 2 +- docs/2021-02/index.html | 2 +- docs/2021-03/index.html | 2 +- docs/2021-04/index.html | 2 +- docs/2021-05/index.html | 2 +- docs/2021-06/index.html | 2 +- docs/2021-07/index.html | 2 +- docs/2021-08/index.html | 2 +- docs/2021-09/index.html | 2 +- docs/2021-10/index.html | 2 +- docs/2021-11/index.html | 2 +- docs/2021-12/index.html | 2 +- docs/2022-01/index.html | 2 +- docs/2022-02/index.html | 2 +- docs/2022-03/index.html | 2 +- docs/2022-04/index.html | 2 +- docs/2022-05/index.html | 2 +- docs/2022-06/index.html | 24 ++++---- docs/2022-07/index.html | 2 +- docs/2022-08/index.html | 67 ++++++++++++++++++++-- docs/404.html | 2 +- docs/categories/index.html | 4 +- docs/categories/notes/index.html | 4 +- docs/categories/notes/page/2/index.html | 4 +- docs/categories/notes/page/3/index.html | 4 +- docs/categories/notes/page/4/index.html | 4 +- docs/categories/notes/page/5/index.html | 4 +- docs/categories/notes/page/6/index.html | 4 +- docs/categories/notes/page/7/index.html | 4 +- docs/cgiar-library-migration/index.html | 2 +- docs/cgspace-cgcorev2-migration/index.html | 2 +- docs/cgspace-dspace6-upgrade/index.html | 2 +- docs/index.html | 4 +- docs/page/2/index.html | 4 +- docs/page/3/index.html | 4 +- docs/page/4/index.html | 4 +- docs/page/5/index.html | 4 +- docs/page/6/index.html | 4 +- docs/page/7/index.html | 4 +- docs/page/8/index.html | 4 +- docs/page/9/index.html | 4 +- docs/posts/index.html | 4 +- docs/posts/page/2/index.html | 4 +- docs/posts/page/3/index.html | 4 +- docs/posts/page/4/index.html | 4 +- docs/posts/page/5/index.html | 4 +- docs/posts/page/6/index.html | 4 +- docs/posts/page/7/index.html | 4 +- docs/posts/page/8/index.html | 4 +- docs/posts/page/9/index.html | 4 +- docs/sitemap.xml | 10 ++-- docs/tags/index.html | 2 +- docs/tags/migration/index.html | 2 +- docs/tags/notes/index.html | 2 +- docs/tags/notes/page/2/index.html | 2 +- docs/tags/notes/page/3/index.html | 2 +- themes/hugo-theme-bootstrap4-blog | 2 +- 121 files changed, 275 insertions(+), 164 deletions(-) diff --git a/content/posts/2022-06.md b/content/posts/2022-06.md index 087788205..3a9c436ef 100644 --- a/content/posts/2022-06.md +++ b/content/posts/2022-06.md @@ -224,7 +224,7 @@ $ ./ilri/agrovoc-lookup.py -i /tmp/2022-06-28-cgspace-subjects.txt -o /tmp/2022- - I had to try in different Python versions because 3.10.x is apparently too new - For future reference I was able to search with lightrdf: -```console +```python import lightrdf parser = lightrdf.Parser() # prints millions of lines diff --git a/content/posts/2022-08.md b/content/posts/2022-08.md index e3eb04f46..44ab18351 100644 --- a/content/posts/2022-08.md +++ b/content/posts/2022-08.md @@ -11,4 +11,56 @@ categories: ["Notes"] +## 2022-08-02 + +- Resume working on the MARLO Innovations + - Last week Jose had sent me an updated CSV with UTF-8 formatting, which was missing the filename column + - I joined it with the older file (stripped down to just the `cg.number` and `filename` columns and then did the same cleanups I had done last week + - I noticed there are six PDFs unused, so I asked Jose +- Spent some time trying to understand the REST API submission issues that Rafael from CIAT is having with tip-approve and tip-submit + - First, according to my notes in 2020-10, a user must be a *collection admin* in order to submit via the REST API + - Second, a collection must have a "Accept/Reject/Edit Metadata" step defined in the workflow + - Also, I referenced my notes from this gist I had made for exactly this purpose! https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a + +## 2022-08-03 + +- I came up with an interesting idea to add missing countries and AGROVOC terms to the MARLO Innovation metadata + - I copied the abstract column to two new fields: `countrytest` and `agrovoctest` and then used this Jython code as a transform to drop terms that don't match (using CGSpace's country list and list of 1,400 AGROVOC terms): + +```python +with open(r"/tmp/cgspace-countries.txt",'r') as f : + countries = [name.rstrip().lower() for name in f] + +return "||".join([x for x in value.split(' ') if x.lower() in countries]) +``` + +- Then I joined them with the other country and AGROVOC columns + - I had originally tried to use csv-metadata-quality to look up and drop invalid AGROVOC terms but it was timing out ever dozen or so requests + - Then I briefly tried to use lightrdf to export a text file of labels from AGROVOC's RDF, but I couldn't figure it out + - I just realized this will not match countries with spaces in our cell value, ugh... and Jython has weird syntax and errors and I can't get normal Python code to work here, I'm missing something +- Then I extracted the titles, dates, and types and added IDs, then ran them through `check-duplicates.py` to find the existing items on CGSpace so I can add them as `dcterm.relation` links + +```console +$ csvcut -l -c dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-08-03-Innovations-Cleaned.csv | sed '1s/line_number/id/' > /tmp/innovations-temp.csv +$ ./ilri/check-duplicates.py -i /tmp/innovations-temp.csv -u dspacetest -db dspacetest -p 'dom@in34sniper' -o /tmp/ccafs-duplicates.csv +``` + +- There were about 115 with existing items on CGSpace +- Then I did some minor processing and checking of the duplicates file (for example, some titles appear more than once in both files), and joined with the other file (left join): + +```console +$ csvjoin --left -c dc.title ~/Downloads/2022-08-03-Innovations-Cleaned.csv ~/Downloads/2022-08-03-Innovations-relations.csv > /tmp/innovations-with-relations.csv +``` + +- Then I used SAFBuilder to create a SimpleItemArchive and import to DSpace Test: + +```console +$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m" +$ dspace import --add --eperson=aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile=./2022-08-03-innovations.map +``` + +- Meeting with Mohammed Salem about harmonizing MEL and CGSpace metadata fields + - I still need to share our results and recommendations with Peter, Enrico, Sara, Svetlana, et al +- I made some minor fixes to csv-metadata-quality while working on the MARLO CRP Innovations + diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index d53940651..dcf4bdc1d 100644 --- a/docs/2015-11/index.html +++ b/docs/2015-11/index.html @@ -64,7 +64,7 @@ $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspac - + diff --git a/docs/2015-12/index.html b/docs/2015-12/index.html index 6e3b85df0..14c774033 100644 --- a/docs/2015-12/index.html +++ b/docs/2015-12/index.html @@ -66,7 +66,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less - + diff --git a/docs/2016-01/index.html b/docs/2016-01/index.html index c5fca3a0f..170582049 100644 --- a/docs/2016-01/index.html +++ b/docs/2016-01/index.html @@ -58,7 +58,7 @@ Update GitHub wiki for documentation of maintenance tasks. - + diff --git a/docs/2016-02/index.html b/docs/2016-02/index.html index 48d6bb360..54dda7eb3 100644 --- a/docs/2016-02/index.html +++ b/docs/2016-02/index.html @@ -68,7 +68,7 @@ Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE&r - + diff --git a/docs/2016-03/index.html b/docs/2016-03/index.html index 65303b060..4a1ca389d 100644 --- a/docs/2016-03/index.html +++ b/docs/2016-03/index.html @@ -58,7 +58,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja - + diff --git a/docs/2016-04/index.html b/docs/2016-04/index.html index 892209e75..afb82e4d3 100644 --- a/docs/2016-04/index.html +++ b/docs/2016-04/index.html @@ -62,7 +62,7 @@ Also, I noticed the checker log has some errors we should pay attention to: - + diff --git a/docs/2016-05/index.html b/docs/2016-05/index.html index b0265fa27..20127c37c 100644 --- a/docs/2016-05/index.html +++ b/docs/2016-05/index.html @@ -64,7 +64,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period! - + diff --git a/docs/2016-06/index.html b/docs/2016-06/index.html index f5c55e73c..4a62600a0 100644 --- a/docs/2016-06/index.html +++ b/docs/2016-06/index.html @@ -64,7 +64,7 @@ Working on second phase of metadata migration, looks like this will work for mov - + diff --git a/docs/2016-07/index.html b/docs/2016-07/index.html index cbf24800f..49f1fb4cc 100644 --- a/docs/2016-07/index.html +++ b/docs/2016-07/index.html @@ -74,7 +74,7 @@ In this case the select query was showing 95 results before the update - + diff --git a/docs/2016-08/index.html b/docs/2016-08/index.html index d5f90d405..8b8e0cd66 100644 --- a/docs/2016-08/index.html +++ b/docs/2016-08/index.html @@ -72,7 +72,7 @@ $ git rebase -i dspace-5.5 - + diff --git a/docs/2016-09/index.html b/docs/2016-09/index.html index 201232320..421002455 100644 --- a/docs/2016-09/index.html +++ b/docs/2016-09/index.html @@ -64,7 +64,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org - + diff --git a/docs/2016-10/index.html b/docs/2016-10/index.html index 45dd1dec8..df1236997 100644 --- a/docs/2016-10/index.html +++ b/docs/2016-10/index.html @@ -72,7 +72,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id - + diff --git a/docs/2016-11/index.html b/docs/2016-11/index.html index c77868dcc..1baa2c0e2 100644 --- a/docs/2016-11/index.html +++ b/docs/2016-11/index.html @@ -56,7 +56,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module - + diff --git a/docs/2016-12/index.html b/docs/2016-12/index.html index c13ba28e1..d02a1f5a9 100644 --- a/docs/2016-12/index.html +++ b/docs/2016-12/index.html @@ -76,7 +76,7 @@ Another worrying error from dspace.log is: - + diff --git a/docs/2017-01/index.html b/docs/2017-01/index.html index 27816ae09..4844dd629 100644 --- a/docs/2017-01/index.html +++ b/docs/2017-01/index.html @@ -58,7 +58,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua - + diff --git a/docs/2017-02/index.html b/docs/2017-02/index.html index 2c00faafb..de295241a 100644 --- a/docs/2017-02/index.html +++ b/docs/2017-02/index.html @@ -80,7 +80,7 @@ Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name - + diff --git a/docs/2017-03/index.html b/docs/2017-03/index.html index d4de56ac4..2fb534898 100644 --- a/docs/2017-03/index.html +++ b/docs/2017-03/index.html @@ -84,7 +84,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg - + diff --git a/docs/2017-04/index.html b/docs/2017-04/index.html index 8e2792a56..9c397f9e1 100644 --- a/docs/2017-04/index.html +++ b/docs/2017-04/index.html @@ -70,7 +70,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thu - + diff --git a/docs/2017-05/index.html b/docs/2017-05/index.html index b79fbf03b..3759eaa4a 100644 --- a/docs/2017-05/index.html +++ b/docs/2017-05/index.html @@ -48,7 +48,7 @@ - + diff --git a/docs/2017-06/index.html b/docs/2017-06/index.html index e2fc5a9fa..43354139f 100644 --- a/docs/2017-06/index.html +++ b/docs/2017-06/index.html @@ -48,7 +48,7 @@ - + diff --git a/docs/2017-07/index.html b/docs/2017-07/index.html index 5cd6de5b7..08685aeb4 100644 --- a/docs/2017-07/index.html +++ b/docs/2017-07/index.html @@ -66,7 +66,7 @@ We can use PostgreSQL’s extended output format (-x) plus sed to format the - + diff --git a/docs/2017-08/index.html b/docs/2017-08/index.html index be8c8e358..9a5edb009 100644 --- a/docs/2017-08/index.html +++ b/docs/2017-08/index.html @@ -90,7 +90,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s - + diff --git a/docs/2017-09/index.html b/docs/2017-09/index.html index 697f30380..a41aa1f39 100644 --- a/docs/2017-09/index.html +++ b/docs/2017-09/index.html @@ -62,7 +62,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account - + diff --git a/docs/2017-10/index.html b/docs/2017-10/index.html index 88e92d459..64b4a5162 100644 --- a/docs/2017-10/index.html +++ b/docs/2017-10/index.html @@ -64,7 +64,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG - + diff --git a/docs/2017-11/index.html b/docs/2017-11/index.html index 0f22d173f..96c6cf95f 100644 --- a/docs/2017-11/index.html +++ b/docs/2017-11/index.html @@ -78,7 +78,7 @@ COPY 54701 - + diff --git a/docs/2017-12/index.html b/docs/2017-12/index.html index 27ce6738d..03d5a105c 100644 --- a/docs/2017-12/index.html +++ b/docs/2017-12/index.html @@ -60,7 +60,7 @@ The list of connections to XMLUI and REST API for today: - + diff --git a/docs/2018-01/index.html b/docs/2018-01/index.html index b94d57a72..37450b7b4 100644 --- a/docs/2018-01/index.html +++ b/docs/2018-01/index.html @@ -180,7 +180,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv - + diff --git a/docs/2018-02/index.html b/docs/2018-02/index.html index fe33b29a9..4dc5e59ac 100644 --- a/docs/2018-02/index.html +++ b/docs/2018-02/index.html @@ -60,7 +60,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-pl - + diff --git a/docs/2018-03/index.html b/docs/2018-03/index.html index c567fe37c..3eb0d057a 100644 --- a/docs/2018-03/index.html +++ b/docs/2018-03/index.html @@ -54,7 +54,7 @@ Export a CSV of the IITA community metadata for Martin Mueller - + diff --git a/docs/2018-04/index.html b/docs/2018-04/index.html index f3697022f..2385ead1b 100644 --- a/docs/2018-04/index.html +++ b/docs/2018-04/index.html @@ -56,7 +56,7 @@ Catalina logs at least show some memory errors yesterday: - + diff --git a/docs/2018-05/index.html b/docs/2018-05/index.html index c7cc815d8..a85bfa220 100644 --- a/docs/2018-05/index.html +++ b/docs/2018-05/index.html @@ -68,7 +68,7 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked - + diff --git a/docs/2018-06/index.html b/docs/2018-06/index.html index 918245295..ab9009e6c 100644 --- a/docs/2018-06/index.html +++ b/docs/2018-06/index.html @@ -88,7 +88,7 @@ sys 2m7.289s - + diff --git a/docs/2018-07/index.html b/docs/2018-07/index.html index d22ac0202..5752bad1d 100644 --- a/docs/2018-07/index.html +++ b/docs/2018-07/index.html @@ -66,7 +66,7 @@ There is insufficient memory for the Java Runtime Environment to continue. - + diff --git a/docs/2018-08/index.html b/docs/2018-08/index.html index a6f1819a1..56120adf9 100644 --- a/docs/2018-08/index.html +++ b/docs/2018-08/index.html @@ -76,7 +76,7 @@ I ran all system updates on DSpace Test and rebooted it - + diff --git a/docs/2018-09/index.html b/docs/2018-09/index.html index ce085fd01..fa6611d0f 100644 --- a/docs/2018-09/index.html +++ b/docs/2018-09/index.html @@ -60,7 +60,7 @@ I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I - + diff --git a/docs/2018-10/index.html b/docs/2018-10/index.html index c7e8e57ca..3def75187 100644 --- a/docs/2018-10/index.html +++ b/docs/2018-10/index.html @@ -56,7 +56,7 @@ I created a GitHub issue to track this #389, because I’m super busy in Nai - + diff --git a/docs/2018-11/index.html b/docs/2018-11/index.html index 50e6dd1fc..3f0888317 100644 --- a/docs/2018-11/index.html +++ b/docs/2018-11/index.html @@ -66,7 +66,7 @@ Today these are the top 10 IPs: - + diff --git a/docs/2018-12/index.html b/docs/2018-12/index.html index 6a8165ae4..6b0d5d089 100644 --- a/docs/2018-12/index.html +++ b/docs/2018-12/index.html @@ -66,7 +66,7 @@ I noticed that there is another issue with PDF thumbnails on CGSpace, and I see - + diff --git a/docs/2019-01/index.html b/docs/2019-01/index.html index 8f64f28be..d9cf0c913 100644 --- a/docs/2019-01/index.html +++ b/docs/2019-01/index.html @@ -80,7 +80,7 @@ I don’t see anything interesting in the web server logs around that time t - + diff --git a/docs/2019-02/index.html b/docs/2019-02/index.html index 9e8a01183..14f8815db 100644 --- a/docs/2019-02/index.html +++ b/docs/2019-02/index.html @@ -102,7 +102,7 @@ sys 0m1.979s - + diff --git a/docs/2019-03/index.html b/docs/2019-03/index.html index b8158a288..951df8c3b 100644 --- a/docs/2019-03/index.html +++ b/docs/2019-03/index.html @@ -76,7 +76,7 @@ I think I will need to ask Udana to re-copy and paste the abstracts with more ca - + diff --git a/docs/2019-04/index.html b/docs/2019-04/index.html index 6369109db..9948c2bdd 100644 --- a/docs/2019-04/index.html +++ b/docs/2019-04/index.html @@ -94,7 +94,7 @@ $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace - + diff --git a/docs/2019-05/index.html b/docs/2019-05/index.html index ae2fcfa3f..5962e315a 100644 --- a/docs/2019-05/index.html +++ b/docs/2019-05/index.html @@ -78,7 +78,7 @@ But after this I tried to delete the item from the XMLUI and it is still present - + diff --git a/docs/2019-06/index.html b/docs/2019-06/index.html index b86321f3b..a50d669aa 100644 --- a/docs/2019-06/index.html +++ b/docs/2019-06/index.html @@ -64,7 +64,7 @@ Skype with Marie-Angélique and Abenet about CG Core v2 - + diff --git a/docs/2019-07/index.html b/docs/2019-07/index.html index 3f78514e8..7003823a5 100644 --- a/docs/2019-07/index.html +++ b/docs/2019-07/index.html @@ -68,7 +68,7 @@ Abenet had another similar issue a few days ago when trying to find the stats fo - + diff --git a/docs/2019-08/index.html b/docs/2019-08/index.html index 50daa889d..6d5137888 100644 --- a/docs/2019-08/index.html +++ b/docs/2019-08/index.html @@ -76,7 +76,7 @@ Run system updates on DSpace Test (linode19) and reboot it - + diff --git a/docs/2019-09/index.html b/docs/2019-09/index.html index 3f2e387da..e16887fe9 100644 --- a/docs/2019-09/index.html +++ b/docs/2019-09/index.html @@ -102,7 +102,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning: - + diff --git a/docs/2019-10/index.html b/docs/2019-10/index.html index 6bc238efc..4adbad41c 100644 --- a/docs/2019-10/index.html +++ b/docs/2019-10/index.html @@ -48,7 +48,7 @@ - + diff --git a/docs/2019-11/index.html b/docs/2019-11/index.html index 19aac491e..733546e02 100644 --- a/docs/2019-11/index.html +++ b/docs/2019-11/index.html @@ -88,7 +88,7 @@ Let’s see how many of the REST API requests were for bitstreams (because t - + diff --git a/docs/2019-12/index.html b/docs/2019-12/index.html index e4d4bb4b9..1f6d0c5a1 100644 --- a/docs/2019-12/index.html +++ b/docs/2019-12/index.html @@ -76,7 +76,7 @@ Make sure all packages are up to date and the package manager is up to date, the - + diff --git a/docs/2020-01/index.html b/docs/2020-01/index.html index faed93e49..ff20c8d2d 100644 --- a/docs/2020-01/index.html +++ b/docs/2020-01/index.html @@ -86,7 +86,7 @@ I tweeted the CGSpace repository link - + diff --git a/docs/2020-02/index.html b/docs/2020-02/index.html index 2f52837ab..f32ad470b 100644 --- a/docs/2020-02/index.html +++ b/docs/2020-02/index.html @@ -68,7 +68,7 @@ The code finally builds and runs with a fresh install - + diff --git a/docs/2020-03/index.html b/docs/2020-03/index.html index 184498087..2a4ade6de 100644 --- a/docs/2020-03/index.html +++ b/docs/2020-03/index.html @@ -72,7 +72,7 @@ You need to download this into the DSpace 6.x source and compile it - + diff --git a/docs/2020-04/index.html b/docs/2020-04/index.html index 23815391d..9018b395c 100644 --- a/docs/2020-04/index.html +++ b/docs/2020-04/index.html @@ -78,7 +78,7 @@ On the same note, the one item Abenet pointed out last week now has a donut with - + diff --git a/docs/2020-05/index.html b/docs/2020-05/index.html index 689878fce..77d47d1d6 100644 --- a/docs/2020-05/index.html +++ b/docs/2020-05/index.html @@ -64,7 +64,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2 - + diff --git a/docs/2020-06/index.html b/docs/2020-06/index.html index dfd254b2b..e64f5e485 100644 --- a/docs/2020-06/index.html +++ b/docs/2020-06/index.html @@ -66,7 +66,7 @@ I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Tes - + diff --git a/docs/2020-07/index.html b/docs/2020-07/index.html index 8a2f6a4ae..6448c7294 100644 --- a/docs/2020-07/index.html +++ b/docs/2020-07/index.html @@ -68,7 +68,7 @@ Since I was restarting Tomcat anyways I decided to redeploy the latest changes f - + diff --git a/docs/2020-08/index.html b/docs/2020-08/index.html index 8feab65f0..587707f2e 100644 --- a/docs/2020-08/index.html +++ b/docs/2020-08/index.html @@ -66,7 +66,7 @@ It is class based so I can easily add support for other vocabularies, and the te - + diff --git a/docs/2020-09/index.html b/docs/2020-09/index.html index 87d82e646..f9d60c4b8 100644 --- a/docs/2020-09/index.html +++ b/docs/2020-09/index.html @@ -78,7 +78,7 @@ I filed an issue on OpenRXV to make some minor edits to the admin UI: https://gi - + diff --git a/docs/2020-10/index.html b/docs/2020-10/index.html index 6f5bbbd3d..1ca11dec2 100644 --- a/docs/2020-10/index.html +++ b/docs/2020-10/index.html @@ -74,7 +74,7 @@ During the FlywayDB migration I got an error: - + diff --git a/docs/2020-11/index.html b/docs/2020-11/index.html index e8caec601..8e28d2319 100644 --- a/docs/2020-11/index.html +++ b/docs/2020-11/index.html @@ -62,7 +62,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat - + diff --git a/docs/2020-12/index.html b/docs/2020-12/index.html index 18010f546..0d3a4bb42 100644 --- a/docs/2020-12/index.html +++ b/docs/2020-12/index.html @@ -66,7 +66,7 @@ I started processing those (about 411,000 records): - + diff --git a/docs/2021-01/index.html b/docs/2021-01/index.html index eddaece1f..83c4aab9b 100644 --- a/docs/2021-01/index.html +++ b/docs/2021-01/index.html @@ -80,7 +80,7 @@ For example, this item has 51 views on CGSpace, but 0 on AReS - + diff --git a/docs/2021-02/index.html b/docs/2021-02/index.html index c5e60043e..80ae1718c 100644 --- a/docs/2021-02/index.html +++ b/docs/2021-02/index.html @@ -90,7 +90,7 @@ $ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty - + diff --git a/docs/2021-03/index.html b/docs/2021-03/index.html index 09a6fecbc..6a5003854 100644 --- a/docs/2021-03/index.html +++ b/docs/2021-03/index.html @@ -64,7 +64,7 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst - + diff --git a/docs/2021-04/index.html b/docs/2021-04/index.html index 7fb4177c6..ca31a0717 100644 --- a/docs/2021-04/index.html +++ b/docs/2021-04/index.html @@ -74,7 +74,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in - + diff --git a/docs/2021-05/index.html b/docs/2021-05/index.html index 500cfc268..1cd7ae2ad 100644 --- a/docs/2021-05/index.html +++ b/docs/2021-05/index.html @@ -66,7 +66,7 @@ I will add the RI/1.0 pattern to our DSpace agents overload and purge them from - + diff --git a/docs/2021-06/index.html b/docs/2021-06/index.html index 4826d164b..5aa429165 100644 --- a/docs/2021-06/index.html +++ b/docs/2021-06/index.html @@ -66,7 +66,7 @@ I simply started it and AReS was running again: - + diff --git a/docs/2021-07/index.html b/docs/2021-07/index.html index d82447975..4dcd1a7a5 100644 --- a/docs/2021-07/index.html +++ b/docs/2021-07/index.html @@ -60,7 +60,7 @@ COPY 20994 - + diff --git a/docs/2021-08/index.html b/docs/2021-08/index.html index aa95202f1..28cc13b87 100644 --- a/docs/2021-08/index.html +++ b/docs/2021-08/index.html @@ -62,7 +62,7 @@ I decided to upgrade linode20 from Ubuntu 18.04 to 20.04 - + diff --git a/docs/2021-09/index.html b/docs/2021-09/index.html index fbf8353ec..470eb08f8 100644 --- a/docs/2021-09/index.html +++ b/docs/2021-09/index.html @@ -78,7 +78,7 @@ The syntax Moayad showed me last month doesn’t seem to honor the search qu - + diff --git a/docs/2021-10/index.html b/docs/2021-10/index.html index abedc88c7..8b81f2590 100644 --- a/docs/2021-10/index.html +++ b/docs/2021-10/index.html @@ -76,7 +76,7 @@ So we have 1879/7100 (26.46%) matching already - + diff --git a/docs/2021-11/index.html b/docs/2021-11/index.html index c84623bd1..fcb6166f1 100644 --- a/docs/2021-11/index.html +++ b/docs/2021-11/index.html @@ -62,7 +62,7 @@ $ zstd statistics-2019.json - + diff --git a/docs/2021-12/index.html b/docs/2021-12/index.html index 9322ce2bb..de17c90da 100644 --- a/docs/2021-12/index.html +++ b/docs/2021-12/index.html @@ -70,7 +70,7 @@ Total number of bot hits purged: 3679 - + diff --git a/docs/2022-01/index.html b/docs/2022-01/index.html index 54af5a4ee..8c9442141 100644 --- a/docs/2022-01/index.html +++ b/docs/2022-01/index.html @@ -54,7 +54,7 @@ Start a full harvest on AReS - + diff --git a/docs/2022-02/index.html b/docs/2022-02/index.html index d4f975291..8141789a0 100644 --- a/docs/2022-02/index.html +++ b/docs/2022-02/index.html @@ -68,7 +68,7 @@ We agreed to try to do more alignment of affiliations/funders with ROR - + diff --git a/docs/2022-03/index.html b/docs/2022-03/index.html index 45314fdef..7591bbb9c 100644 --- a/docs/2022-03/index.html +++ b/docs/2022-03/index.html @@ -64,7 +64,7 @@ $ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv & - + diff --git a/docs/2022-04/index.html b/docs/2022-04/index.html index e470d50e4..5cc4b11a5 100644 --- a/docs/2022-04/index.html +++ b/docs/2022-04/index.html @@ -48,7 +48,7 @@ - + diff --git a/docs/2022-05/index.html b/docs/2022-05/index.html index 5105c72b1..81e620543 100644 --- a/docs/2022-05/index.html +++ b/docs/2022-05/index.html @@ -96,7 +96,7 @@ I purged 93,974 hits from these IPs using my check-spider-ip-hits.sh script - + diff --git a/docs/2022-06/index.html b/docs/2022-06/index.html index 7b8184917..4c4f2dcde 100644 --- a/docs/2022-06/index.html +++ b/docs/2022-06/index.html @@ -78,7 +78,7 @@ There seem to be many more of these: - + @@ -373,19 +373,19 @@ There seem to be many more of these:
  • For future reference I was able to search with lightrdf:
    • -
    import lightrdf
-parser = lightrdf.Parser()
-# prints millions of lines
-for triple in parser.parse("./agrovoc_lod.rdf", base_iri=None):
+
    import lightrdf
+parser = lightrdf.Parser()
+# prints millions of lines
+for triple in parser.parse("./agrovoc_lod.rdf", base_iri=None):
      print(triple)
-agrovoc = lightrdf.RDFDocument('agrovoc_lod.rdf');
-# all results for prefix http://aims.fao.org/aos/agrovoc/c_5
-for triple in agrovoc.search_triples('http://aims.fao.org/aos/agrovoc/c_5', None, None):
+agrovoc = lightrdf.RDFDocument('agrovoc_lod.rdf');
+# all results for prefix http://aims.fao.org/aos/agrovoc/c_5
+for triple in agrovoc.search_triples('http://aims.fao.org/aos/agrovoc/c_5', None, None):
      print(triple)
-('http://aims.fao.org/aos/agrovoc/c_5', 'http://www.w3.org/2004/02/skos/core#altLabel', '"Abalone"@de')
-('http://aims.fao.org/aos/agrovoc/c_5', 'http://www.w3.org/2004/02/skos/core#prefLabel', '"abalones"@en')
-# all stuff for abalones in English
-for triple in agrovoc.search_triples(None, None, '"abalones"@en'):
+('http://aims.fao.org/aos/agrovoc/c_5', 'http://www.w3.org/2004/02/skos/core#altLabel', '"Abalone"@de')
+('http://aims.fao.org/aos/agrovoc/c_5', 'http://www.w3.org/2004/02/skos/core#prefLabel', '"abalones"@en')
+# all stuff for abalones in English
+for triple in agrovoc.search_triples(None, None, '"abalones"@en'):
      print(triple)
 
      
 
    • I ran the agrovoc-lookup.py from a Linode server and it completed without issues… hmmm
      • 
diff --git a/docs/2022-07/index.html b/docs/2022-07/index.html
index 6d3c2ec02..a06836b67 100644
--- a/docs/2022-07/index.html
+++ b/docs/2022-07/index.html
@@ -64,7 +64,7 @@ Also, the trgm functions I’ve used before are case insensitive, but Levens
     
     
     
-    
+    
     
 
     
diff --git a/docs/2022-08/index.html b/docs/2022-08/index.html
index 173672b45..5569fa24c 100644
--- a/docs/2022-08/index.html
+++ b/docs/2022-08/index.html
@@ -14,7 +14,7 @@ Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
 
 
 
-
+
 
 
 
@@ -34,9 +34,9 @@ Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
   "@type": "BlogPosting",
   "headline": "August, 2022",
   "url": "https://alanorth.github.io/cgspace-notes/2022-08/",
-  "wordCount": "14",
+  "wordCount": "492",
   "datePublished": "2022-08-01T10:22:36+03:00",
-  "dateModified": "2022-08-01T10:22:36+03:00",
+  "dateModified": "2022-08-01T16:36:13+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -54,7 +54,7 @@ Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
     
     
     
-    
+    
     
 
     
@@ -114,6 +114,65 @@ Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
 
+
      2022-08-02
      
+
        
+
      • Resume working on the MARLO Innovations
+
          
+
        • Last week Jose had sent me an updated CSV with UTF-8 formatting, which was missing the filename column
          • 
+
        • I joined it with the older file (stripped down to just the cg.number and filename columns and then did the same cleanups I had done last week
          • 
+
        • I noticed there are six PDFs unused, so I asked Jose
          • 
+
        
+
        • 
+
      • Spent some time trying to understand the REST API submission issues that Rafael from CIAT is having with tip-approve and tip-submit
+
          
+
        • First, according to my notes in 2020-10, a user must be a collection admin in order to submit via the REST API
          • 
+
        • Second, a collection must have a “Accept/Reject/Edit Metadata” step defined in the workflow
          • 
+
        • Also, I referenced my notes from this gist I had made for exactly this purpose! https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a
          • 
+
        
+
        • 
+
      
+
      2022-08-03
      
+
        
+
      • I came up with an interesting idea to add missing countries and AGROVOC terms to the MARLO Innovation metadata
+
          
+
        • I copied the abstract column to two new fields: countrytest and agrovoctest and then used this Jython code as a transform to drop terms that don’t match (using CGSpace’s country list and list of 1,400 AGROVOC terms):
          • 
+
        
+
        • 
+
      
+
      with open(r"/tmp/cgspace-countries.txt",'r') as f :
+    countries = [name.rstrip().lower() for name in f]
+
+return "||".join([x for x in value.split(' ') if x.lower() in countries])
+
        
+
      • Then I joined them with the other country and AGROVOC columns
+
          
+
        • I had originally tried to use csv-metadata-quality to look up and drop invalid AGROVOC terms but it was timing out ever dozen or so requests
          • 
+
        • Then I briefly tried to use lightrdf to export a text file of labels from AGROVOC’s RDF, but I couldn’t figure it out
          • 
+
        • I just realized this will not match countries with spaces in our cell value, ugh… and Jython has weird syntax and errors and I can’t get normal Python code to work here, I’m missing something
          • 
+
        
+
        • 
+
      • Then I extracted the titles, dates, and types and added IDs, then ran them through check-duplicates.py to find the existing items on CGSpace so I can add them as dcterm.relation links
        • 
+
      
+
      $ csvcut -l -c dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-08-03-Innovations-Cleaned.csv | sed '1s/line_number/id/' > /tmp/innovations-temp.csv
+$ ./ilri/check-duplicates.py -i /tmp/innovations-temp.csv -u dspacetest -db dspacetest -p 'dom@in34sniper' -o /tmp/ccafs-duplicates.csv
+
        
+
      • There were about 115 with existing items on CGSpace
        • 
+
      • Then I did some minor processing and checking of the duplicates file (for example, some titles appear more than once in both files), and joined with the other file (left join):
        • 
+
      
+
      $ csvjoin --left -c dc.title ~/Downloads/2022-08-03-Innovations-Cleaned.csv ~/Downloads/2022-08-03-Innovations-relations.csv > /tmp/innovations-with-relations.csv
+
        
+
      • Then I used SAFBuilder to create a SimpleItemArchive and import to DSpace Test:
        • 
+
      
+
      $ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m"
+$ dspace import --add --eperson=aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile=./2022-08-03-innovations.map
+
        
+
      • Meeting with Mohammed Salem about harmonizing MEL and CGSpace metadata fields
+
          
+
        • I still need to share our results and recommendations with Peter, Enrico, Sara, Svetlana, et al
          • 
+
        
+
        • 
+
      • I made some minor fixes to csv-metadata-quality while working on the MARLO CRP Innovations
        • 
+
      
 
 
   
diff --git a/docs/404.html b/docs/404.html
index ff00cacf2..447cbe6eb 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -31,7 +31,7 @@
     
     
     
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diff --git a/docs/categories/index.html b/docs/categories/index.html
index c8b3c36f5..be15a46ea 100644
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index 3417f1e22..de3dc6268 100644
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index c3ba37eef..e85cd89fb 100644
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index a9c378941..88fe35a14 100644
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index 081b3597d..9d7814b7b 100644
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index 174100d39..ac654a6ab 100644
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