diff --git a/content/posts/2021-06.md b/content/posts/2021-06.md index b4f41ce93..4ce1b6ba5 100644 --- a/content/posts/2021-06.md +++ b/content/posts/2021-06.md @@ -87,7 +87,7 @@ $ podman unshare chown 1000:1000 /home/aorth/.local/share/containers/storage/vol - The new OpenRXV harvesting method by Moayad uses pages of 10 items instead of 100 and it's much faster - I harvested 90,000+ items from DSpace Test in ~3 hours - - There seem to be some issues with the health check step though + - There seem to be some issues with the health check step though, as I see it is requesting one restricted item 600,000+ times... ## 2021-06-17 @@ -116,4 +116,83 @@ $ grep -oE '"handle":"[[:digit:]]+/[[:digit:]]+"' openrxv-items_data.json | awk 3 "10568/96546" ``` +## 2021-06-20 + +- Udana asked me to update their IWMI subjects from `farmer managed irrigation systems` to `farmer-led irrigation` + - First I extracted the IWMI community from CGSpace: + +```console +$ dspace metadata-export -i 10568/16814 -f /tmp/2021-06-20-IWMI.csv +``` + +- Then I used `csvcut` to extract just the columns I needed and do the replacement into a new CSV: + +```console +$ csvcut -c 'id,dcterms.subject[],dcterms.subject[en_US]' /tmp/2021-06-20-IWMI.csv | sed 's/farmer managed irrigation systems/farmer-led irrigation/' > /tmp/2021-06-20-IWMI-new-subjects.csv +``` + +- Then I uploaded the resulting CSV to CGSpace, updating 161 items +- Start a harvest on AReS +- I found [a bug](https://jira.lyrasis.org/browse/DS-1977) and [a patch](https://github.com/DSpace/DSpace/pull/2584) for the private items showing up in the DSpace sitemap bug + - The fix is super simple, I should try to apply it + +## 2021-06-21 + +- The AReS harvesting finished, but the indexes got messed up again +- I was looking at the JSON export I made yesterday and trying to understand the situation with duplicates + - We have 90,000+ items, but only 85,000 unique: + +```console +$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | wc -l +90937 +$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | sort -u | wc -l +85709 +``` + +- So those could be duplicates from the way we harvest pages, but they could also be from mappings... + - Manually inspecting the duplicates where handles appear more than once: + +```console +$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | sort | uniq -c | sort -h +``` + +- Unfortunately I found no pattern: + - Some appear twice in the Elasticsearch index, but appear in only one collection + - Some appear twice in the Elasticsearch index, and appear in *two* collections + - Some appear twice in the Elasticsearch index, but appear in three collections (!) +- So really we need to just check whether a handle exists before we insert it +- I tested the [pull request for DS-1977](https://github.com/DSpace/DSpace/pull/2584) that adjusts the sitemap generation code to exclude private items + - It applies cleanly and seems to work, but we don't actually have any private items + - The issue we are having with AReS hitting restricted items in the sitemap is that the items have restricted metadata, not that they are private +- Testing the [pull request for DS-4065](https://github.com/DSpace/DSpace/pull/2275) where the REST API's `/rest/items` endpoint is not aware of private items and returns an incorrect number of items + - This is most easily seen by setting a low limit in `/rest/items`, making one of the items private, and requesting items again with the same limit + - I confirmed the issue on the current DSpace 6 Demo: + +```console +$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq length +5 +$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq '.[].handle' +"10673/4" +"10673/3" +"10673/6" +"10673/5" +"10673/7" +# log into DSpace Demo XMLUI as admin and make one item private (for example 10673/6) +$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq length +4 +$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq '.[].handle' +"10673/4" +"10673/3" +"10673/5" +"10673/7" +``` + +- I tested the pull request on DSpace Test and it works, so I left a note on GitHub and Jira +- Last week I noticed that the Gender Platform website is using "cgspace.cgiar.org" links for CGSpace, instead of handles + - I emailed Fabio and Marianne to ask them to please use the Handle links +- I tested the [pull request for DS-4271](https://github.com/DSpace/DSpace/pull/2543) where Discovery filters of type "contains" don't work as expected when the user's search term has spaces + - I tested with filter "farmer managed irrigation systems" on DSpace Test + - Before the patch I got 293 results, and the few I checked didn't have the expected metadata value + - After the patch I got 162 results, and all the items I checked had the exact metadata value I was expecting + diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index a3f696f86..c326f865f 100644 --- a/docs/2015-11/index.html +++ b/docs/2015-11/index.html @@ -34,7 +34,7 @@ Last week I had increased the limit from 30 to 60, which seemed to help, but now $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace 78 "/> - + diff --git a/docs/2015-12/index.html b/docs/2015-12/index.html index ab493b975..5ebb3f427 100644 --- a/docs/2015-12/index.html +++ b/docs/2015-12/index.html @@ -36,7 +36,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less -rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo -rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz "/> - + diff --git a/docs/2016-01/index.html b/docs/2016-01/index.html index 383285b4c..854dcfcd1 100644 --- a/docs/2016-01/index.html +++ b/docs/2016-01/index.html @@ -28,7 +28,7 @@ Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_ I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated. Update GitHub wiki for documentation of maintenance tasks. "/> - + diff --git a/docs/2016-02/index.html b/docs/2016-02/index.html index 48119c6f4..bcc920218 100644 --- a/docs/2016-02/index.html +++ b/docs/2016-02/index.html @@ -38,7 +38,7 @@ I noticed we have a very interesting list of countries on CGSpace: Not only are there 49,000 countries, we have some blanks (25)… Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE” "/> - + diff --git a/docs/2016-03/index.html b/docs/2016-03/index.html index 2817a2717..c81ce934f 100644 --- a/docs/2016-03/index.html +++ b/docs/2016-03/index.html @@ -28,7 +28,7 @@ Looking at issues with author authorities on CGSpace For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server "/> - + diff --git a/docs/2016-04/index.html b/docs/2016-04/index.html index 36451888b..38a38e39c 100644 --- a/docs/2016-04/index.html +++ b/docs/2016-04/index.html @@ -32,7 +32,7 @@ After running DSpace for over five years I’ve never needed to look in any This will save us a few gigs of backup space we’re paying for on S3 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 9be872ba1..09277d469 100644 --- a/docs/2016-05/index.html +++ b/docs/2016-05/index.html @@ -34,7 +34,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period! # awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l 3168 "/> - + diff --git a/docs/2016-06/index.html b/docs/2016-06/index.html index fe74376f9..4e62cc7e5 100644 --- a/docs/2016-06/index.html +++ b/docs/2016-06/index.html @@ -34,7 +34,7 @@ This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRec You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship "/> - + diff --git a/docs/2016-07/index.html b/docs/2016-07/index.html index ba145c7cc..841958f16 100644 --- a/docs/2016-07/index.html +++ b/docs/2016-07/index.html @@ -44,7 +44,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and 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 cd8e162e5..1c3844afe 100644 --- a/docs/2016-08/index.html +++ b/docs/2016-08/index.html @@ -42,7 +42,7 @@ $ git checkout -b 55new 5_x-prod $ git reset --hard ilri/5_x-prod $ git rebase -i dspace-5.5 "/> - + diff --git a/docs/2016-09/index.html b/docs/2016-09/index.html index 391c75425..6b6f1cf9e 100644 --- a/docs/2016-09/index.html +++ b/docs/2016-09/index.html @@ -34,7 +34,7 @@ It looks like we might be able to use OUs now, instead of DCs: $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)" "/> - + diff --git a/docs/2016-10/index.html b/docs/2016-10/index.html index c7c61f345..48945f38d 100644 --- a/docs/2016-10/index.html +++ b/docs/2016-10/index.html @@ -42,7 +42,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X "/> - + diff --git a/docs/2016-11/index.html b/docs/2016-11/index.html index 6810d192e..eea31ee65 100644 --- a/docs/2016-11/index.html +++ b/docs/2016-11/index.html @@ -26,7 +26,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module Add dc.type to the output options for Atmire’s Listings and Reports module (#286) "/> - + diff --git a/docs/2016-12/index.html b/docs/2016-12/index.html index d65879f4e..b4de7627a 100644 --- a/docs/2016-12/index.html +++ b/docs/2016-12/index.html @@ -46,7 +46,7 @@ I see thousands of them in the logs for the last few months, so it’s not r I’ve raised a ticket with Atmire to ask Another worrying error from dspace.log is: "/> - + diff --git a/docs/2017-01/index.html b/docs/2017-01/index.html index 022b86b86..d253f5cb9 100644 --- a/docs/2017-01/index.html +++ b/docs/2017-01/index.html @@ -28,7 +28,7 @@ I checked to see if the Solr sharding task that is supposed to run on January 1s I tested on DSpace Test as well and it doesn’t work there either I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years "/> - + diff --git a/docs/2017-02/index.html b/docs/2017-02/index.html index 064da78bd..ca465f1b1 100644 --- a/docs/2017-02/index.html +++ b/docs/2017-02/index.html @@ -50,7 +50,7 @@ DELETE 1 Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301) 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 e31d38a3c..ed27b212a 100644 --- a/docs/2017-03/index.html +++ b/docs/2017-03/index.html @@ -54,7 +54,7 @@ Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing reg $ identify ~/Desktop/alc_contrastes_desafios.jpg /Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000 "/> - + diff --git a/docs/2017-04/index.html b/docs/2017-04/index.html index 03837bc96..d433e36f6 100644 --- a/docs/2017-04/index.html +++ b/docs/2017-04/index.html @@ -40,7 +40,7 @@ Testing the CMYK patch on a collection with 650 items: $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt "/> - + diff --git a/docs/2017-05/index.html b/docs/2017-05/index.html index b8eeff1e9..c01476b2e 100644 --- a/docs/2017-05/index.html +++ b/docs/2017-05/index.html @@ -18,7 +18,7 @@ - + diff --git a/docs/2017-06/index.html b/docs/2017-06/index.html index bbfd3e965..6f4ce11c9 100644 --- a/docs/2017-06/index.html +++ b/docs/2017-06/index.html @@ -18,7 +18,7 @@ - + diff --git a/docs/2017-07/index.html b/docs/2017-07/index.html index 4de6630d9..e3aed40a7 100644 --- a/docs/2017-07/index.html +++ b/docs/2017-07/index.html @@ -36,7 +36,7 @@ Merge changes for WLE Phase II theme rename (#329) Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML: "/> - + diff --git a/docs/2017-08/index.html b/docs/2017-08/index.html index d82226800..ec6c59cdb 100644 --- a/docs/2017-08/index.html +++ b/docs/2017-08/index.html @@ -60,7 +60,7 @@ This was due to newline characters in the dc.description.abstract column, which I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet "/> - + diff --git a/docs/2017-09/index.html b/docs/2017-09/index.html index f235de65e..52394e6df 100644 --- a/docs/2017-09/index.html +++ b/docs/2017-09/index.html @@ -32,7 +32,7 @@ Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group "/> - + diff --git a/docs/2017-10/index.html b/docs/2017-10/index.html index ff693e213..b268e4412 100644 --- a/docs/2017-10/index.html +++ b/docs/2017-10/index.html @@ -34,7 +34,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336 There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections "/> - + diff --git a/docs/2017-11/index.html b/docs/2017-11/index.html index 66ed1f113..d5c6ffd83 100644 --- a/docs/2017-11/index.html +++ b/docs/2017-11/index.html @@ -48,7 +48,7 @@ Generate list of authors on CGSpace for Peter to go through and correct: dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv; COPY 54701 "/> - + diff --git a/docs/2017-12/index.html b/docs/2017-12/index.html index 8bb578f21..1892c7e0d 100644 --- a/docs/2017-12/index.html +++ b/docs/2017-12/index.html @@ -30,7 +30,7 @@ The logs say “Timeout waiting for idle object” PostgreSQL activity says there are 115 connections currently 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 75f0cd4cd..3e22cd52b 100644 --- a/docs/2018-01/index.html +++ b/docs/2018-01/index.html @@ -150,7 +150,7 @@ dspace.log.2018-01-02:34 Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains "/> - + diff --git a/docs/2018-02/index.html b/docs/2018-02/index.html index ef7f9ff2f..c0cbc1ac0 100644 --- a/docs/2018-02/index.html +++ b/docs/2018-02/index.html @@ -30,7 +30,7 @@ We don’t need to distinguish between internal and external works, so that Yesterday I figured out how to monitor DSpace sessions using JMX I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01 "/> - + diff --git a/docs/2018-03/index.html b/docs/2018-03/index.html index 424dedc05..a886a3bf1 100644 --- a/docs/2018-03/index.html +++ b/docs/2018-03/index.html @@ -24,7 +24,7 @@ Export a CSV of the IITA community metadata for Martin Mueller 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 95b5c3a28..4c0c8f161 100644 --- a/docs/2018-04/index.html +++ b/docs/2018-04/index.html @@ -26,7 +26,7 @@ Catalina logs at least show some memory errors yesterday: I tried to test something on DSpace Test but noticed that it’s down since god knows when Catalina logs at least show some memory errors yesterday: "/> - + diff --git a/docs/2018-05/index.html b/docs/2018-05/index.html index 841bc3a6e..fd6d28642 100644 --- a/docs/2018-05/index.html +++ b/docs/2018-05/index.html @@ -38,7 +38,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E Then I reduced the JVM heap size from 6144 back to 5120m Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use "/> - + diff --git a/docs/2018-06/index.html b/docs/2018-06/index.html index 99451b9a0..edefbee40 100644 --- a/docs/2018-06/index.html +++ b/docs/2018-06/index.html @@ -58,7 +58,7 @@ real 74m42.646s user 8m5.056s sys 2m7.289s "/> - + diff --git a/docs/2018-07/index.html b/docs/2018-07/index.html index 7c3fd56c6..c7c3e4693 100644 --- a/docs/2018-07/index.html +++ b/docs/2018-07/index.html @@ -36,7 +36,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r 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 765404717..b7687fbde 100644 --- a/docs/2018-08/index.html +++ b/docs/2018-08/index.html @@ -46,7 +46,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes 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 8199526e3..9a388b3ce 100644 --- a/docs/2018-09/index.html +++ b/docs/2018-09/index.html @@ -30,7 +30,7 @@ I’ll update the DSpace role in our Ansible infrastructure playbooks and ru Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again: "/> - + diff --git a/docs/2018-10/index.html b/docs/2018-10/index.html index ad2141b28..68a459818 100644 --- a/docs/2018-10/index.html +++ b/docs/2018-10/index.html @@ -26,7 +26,7 @@ I created a GitHub issue to track this #389, because I’m super busy in Nai Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items I created a GitHub issue to track this #389, because I’m super busy in Nairobi right now "/> - + diff --git a/docs/2018-11/index.html b/docs/2018-11/index.html index e784c3cda..0728b79b4 100644 --- a/docs/2018-11/index.html +++ b/docs/2018-11/index.html @@ -36,7 +36,7 @@ Send a note about my dspace-statistics-api to the dspace-tech mailing list Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage Today these are the top 10 IPs: "/> - + diff --git a/docs/2018-12/index.html b/docs/2018-12/index.html index 997679551..899cfa117 100644 --- a/docs/2018-12/index.html +++ b/docs/2018-12/index.html @@ -36,7 +36,7 @@ Then I ran all system updates and restarted the server I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week "/> - + diff --git a/docs/2019-01/index.html b/docs/2019-01/index.html index ebc17255f..dbd20bae3 100644 --- a/docs/2019-01/index.html +++ b/docs/2019-01/index.html @@ -50,7 +50,7 @@ I don’t see anything interesting in the web server logs around that time t 357 207.46.13.1 903 54.70.40.11 "/> - + diff --git a/docs/2019-02/index.html b/docs/2019-02/index.html index 2ab70b40e..ecef61d19 100644 --- a/docs/2019-02/index.html +++ b/docs/2019-02/index.html @@ -72,7 +72,7 @@ real 0m19.873s user 0m22.203s sys 0m1.979s "/> - + diff --git a/docs/2019-03/index.html b/docs/2019-03/index.html index 5c37cc331..919280f4b 100644 --- a/docs/2019-03/index.html +++ b/docs/2019-03/index.html @@ -46,7 +46,7 @@ Most worryingly, there are encoding errors in the abstracts for eleven items, fo I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs "/> - + diff --git a/docs/2019-04/index.html b/docs/2019-04/index.html index 5a5b04b08..ff4227e2b 100644 --- a/docs/2019-04/index.html +++ b/docs/2019-04/index.html @@ -64,7 +64,7 @@ $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u ds $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p 'fuuu' -m 228 -f cg.coverage.country -d $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p 'fuuu' -m 231 -f cg.coverage.region -d "/> - + diff --git a/docs/2019-05/index.html b/docs/2019-05/index.html index 5d3df8450..97a53871e 100644 --- a/docs/2019-05/index.html +++ b/docs/2019-05/index.html @@ -48,7 +48,7 @@ DELETE 1 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 ad13e36ff..73bc667f5 100644 --- a/docs/2019-06/index.html +++ b/docs/2019-06/index.html @@ -34,7 +34,7 @@ Run system updates on CGSpace (linode18) and reboot it 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 d01f0082c..d09478215 100644 --- a/docs/2019-07/index.html +++ b/docs/2019-07/index.html @@ -38,7 +38,7 @@ CGSpace Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community "/> - + diff --git a/docs/2019-08/index.html b/docs/2019-08/index.html index c4eb2e4f9..33effbeeb 100644 --- a/docs/2019-08/index.html +++ b/docs/2019-08/index.html @@ -46,7 +46,7 @@ After rebooting, all statistics cores were loaded… wow, that’s luck 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 611d1d91c..fa45545ec 100644 --- a/docs/2019-09/index.html +++ b/docs/2019-09/index.html @@ -72,7 +72,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning: 7249 2a01:7e00::f03c:91ff:fe18:7396 9124 45.5.186.2 "/> - + diff --git a/docs/2019-10/index.html b/docs/2019-10/index.html index c30f1da29..61219617e 100644 --- a/docs/2019-10/index.html +++ b/docs/2019-10/index.html @@ -18,7 +18,7 @@ - + diff --git a/docs/2019-11/index.html b/docs/2019-11/index.html index 8a3955f0e..b034765dd 100644 --- a/docs/2019-11/index.html +++ b/docs/2019-11/index.html @@ -58,7 +58,7 @@ Let’s see how many of the REST API requests were for bitstreams (because t # zcat --force /var/log/nginx/rest.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep -c -E "/rest/bitstreams" 106781 "/> - + diff --git a/docs/2019-12/index.html b/docs/2019-12/index.html index c43ccbde7..1c434579a 100644 --- a/docs/2019-12/index.html +++ b/docs/2019-12/index.html @@ -46,7 +46,7 @@ Make sure all packages are up to date and the package manager is up to date, the # dpkg -C # reboot "/> - + diff --git a/docs/2020-01/index.html b/docs/2020-01/index.html index cf9842ad9..2e188d7b5 100644 --- a/docs/2020-01/index.html +++ b/docs/2020-01/index.html @@ -56,7 +56,7 @@ I tweeted the CGSpace repository link "/> - + diff --git a/docs/2020-02/index.html b/docs/2020-02/index.html index 3bc43f5eb..5e99847d1 100644 --- a/docs/2020-02/index.html +++ b/docs/2020-02/index.html @@ -38,7 +38,7 @@ 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 1160f27c7..433497a9b 100644 --- a/docs/2020-03/index.html +++ b/docs/2020-03/index.html @@ -42,7 +42,7 @@ 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 ec4a0638b..4edea74d7 100644 --- a/docs/2020-04/index.html +++ b/docs/2020-04/index.html @@ -48,7 +48,7 @@ The third item now has a donut with score 1 since I tweeted it last week On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week "/> - + diff --git a/docs/2020-05/index.html b/docs/2020-05/index.html index bce8e214e..fa2c22238 100644 --- a/docs/2020-05/index.html +++ b/docs/2020-05/index.html @@ -34,7 +34,7 @@ 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 a2d853bb4..32540abe5 100644 --- a/docs/2020-06/index.html +++ b/docs/2020-06/index.html @@ -36,7 +36,7 @@ I sent Atmire the dspace.log from today and told them to log into the server to In other news, I checked the statistics API on DSpace 6 and it’s working I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error: "/> - + diff --git a/docs/2020-07/index.html b/docs/2020-07/index.html index a8802d285..cc2245ba4 100644 --- a/docs/2020-07/index.html +++ b/docs/2020-07/index.html @@ -38,7 +38,7 @@ I restarted Tomcat and PostgreSQL and the issue was gone Since I was restarting Tomcat anyways I decided to redeploy the latest changes from the 5_x-prod branch and I added a note about COVID-19 items to the CGSpace frontpage at Peter’s request "/> - + diff --git a/docs/2020-08/index.html b/docs/2020-08/index.html index 91641eb07..89591419a 100644 --- a/docs/2020-08/index.html +++ b/docs/2020-08/index.html @@ -36,7 +36,7 @@ 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 f2dc410f4..a75648e8d 100644 --- a/docs/2020-09/index.html +++ b/docs/2020-09/index.html @@ -48,7 +48,7 @@ I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39 I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40 "/> - + diff --git a/docs/2020-10/index.html b/docs/2020-10/index.html index 18cdeb89c..88b609592 100644 --- a/docs/2020-10/index.html +++ b/docs/2020-10/index.html @@ -44,7 +44,7 @@ During the FlywayDB migration I got an error: "/> - + @@ -723,14 +723,14 @@ data = json.# acronym_pattern = re.compile(r"[A-Z]+$") acronym_pattern_match = acronym_pattern.search(replace) - if acronym_pattern_match is not None: + if acronym_pattern_match is not None: continue mapping = { "find": find, "replace": replace } # Print command for Elasticsearch - print('{"index":{}}') - print(json.dumps(mapping)) + print('{"index":{}}') + print(json.dumps(mapping)) f.close() @@ -247,7 +247,103 @@ $ grep -oE '"handle":"[[:digit:]]+/[[:digit:]]+"' openrxv-it 3 "10568/106940" 3 "10568/107195" 3 "10568/96546" - +

2021-06-20

+ +
$ dspace metadata-export -i 10568/16814 -f /tmp/2021-06-20-IWMI.csv
+
+
$ csvcut -c 'id,dcterms.subject[],dcterms.subject[en_US]' /tmp/2021-06-20-IWMI.csv | sed 's/farmer managed irrigation systems/farmer-led irrigation/' > /tmp/2021-06-20-IWMI-new-subjects.csv
+
+

2021-06-21

+ +
$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | wc -l
+90937
+$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | sort -u | wc -l
+85709
+
+
$ grep -E '"repo":"CGSpace"' openrxv-items_data.json | grep -oE '"handle":"[[:digit:]]+/[[:alnum:]]+"' | sort | uniq -c | sort -h
+
+
$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq length
+5
+$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq '.[].handle'
+"10673/4"
+"10673/3"
+"10673/6"
+"10673/5"
+"10673/7"
+# log into DSpace Demo XMLUI as admin and make one item private (for example 10673/6)
+$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq length       
+4
+$ curl -s -H "Accept: application/json" "https://demo.dspace.org/rest/items?offset=0&limit=5" | jq '.[].handle' 
+"10673/4"
+"10673/3"
+"10673/5"
+"10673/7"
+
+ diff --git a/docs/404.html b/docs/404.html index ec6388e03..bd3936075 100644 --- a/docs/404.html +++ b/docs/404.html @@ -17,7 +17,7 @@ - + diff --git a/docs/categories/index.html b/docs/categories/index.html index a50e4970f..832047628 100644 --- a/docs/categories/index.html +++ b/docs/categories/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/categories/notes/index.html b/docs/categories/notes/index.html index c0df3320a..e79ac811c 100644 --- a/docs/categories/notes/index.html +++ b/docs/categories/notes/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/categories/notes/page/2/index.html b/docs/categories/notes/page/2/index.html index a093b205c..4f92fdb7a 100644 --- a/docs/categories/notes/page/2/index.html +++ b/docs/categories/notes/page/2/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/categories/notes/page/3/index.html b/docs/categories/notes/page/3/index.html index ad69bd0fc..ebc147de4 100644 --- a/docs/categories/notes/page/3/index.html +++ b/docs/categories/notes/page/3/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/categories/notes/page/4/index.html b/docs/categories/notes/page/4/index.html index 08c1ef445..ff16557a1 100644 --- a/docs/categories/notes/page/4/index.html +++ b/docs/categories/notes/page/4/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/categories/notes/page/5/index.html b/docs/categories/notes/page/5/index.html index 5eb4b2a67..d9b0db2ce 100644 --- a/docs/categories/notes/page/5/index.html +++ b/docs/categories/notes/page/5/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/cgiar-library-migration/index.html b/docs/cgiar-library-migration/index.html index 1d403b8e3..f001d6343 100644 --- a/docs/cgiar-library-migration/index.html +++ b/docs/cgiar-library-migration/index.html @@ -18,7 +18,7 @@ - + diff --git a/docs/cgspace-cgcorev2-migration/index.html b/docs/cgspace-cgcorev2-migration/index.html index f21b81b83..b18e29fd0 100644 --- a/docs/cgspace-cgcorev2-migration/index.html +++ b/docs/cgspace-cgcorev2-migration/index.html @@ -18,7 +18,7 @@ - + diff --git a/docs/cgspace-dspace6-upgrade/index.html b/docs/cgspace-dspace6-upgrade/index.html index b1d054071..2021ad566 100644 --- a/docs/cgspace-dspace6-upgrade/index.html +++ b/docs/cgspace-dspace6-upgrade/index.html @@ -18,7 +18,7 @@ - + diff --git a/docs/index.html b/docs/index.html index 6a58929b0..cf3872552 100644 --- a/docs/index.html +++ b/docs/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/page/2/index.html b/docs/page/2/index.html index b644cf2be..6552d9fd8 100644 --- a/docs/page/2/index.html +++ b/docs/page/2/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/page/3/index.html b/docs/page/3/index.html index 48b5d06cd..92a90fb6e 100644 --- a/docs/page/3/index.html +++ b/docs/page/3/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/page/4/index.html b/docs/page/4/index.html index c029300cf..b502ebb5f 100644 --- a/docs/page/4/index.html +++ b/docs/page/4/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/page/5/index.html b/docs/page/5/index.html index 0213ad306..675b88b4d 100644 --- a/docs/page/5/index.html +++ b/docs/page/5/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/page/6/index.html b/docs/page/6/index.html index aa9580600..b34131e22 100644 --- a/docs/page/6/index.html +++ b/docs/page/6/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/page/7/index.html b/docs/page/7/index.html index 294cfc289..5bfce3dab 100644 --- a/docs/page/7/index.html +++ b/docs/page/7/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/page/8/index.html b/docs/page/8/index.html index f1208897f..c13e179d5 100644 --- a/docs/page/8/index.html +++ b/docs/page/8/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/index.html b/docs/posts/index.html index a4ca2bf27..be7067d62 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/page/2/index.html b/docs/posts/page/2/index.html index a9e8e1792..3f0c5ffdf 100644 --- a/docs/posts/page/2/index.html +++ b/docs/posts/page/2/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/page/3/index.html b/docs/posts/page/3/index.html index 44ca45b4d..0295765d3 100644 --- a/docs/posts/page/3/index.html +++ b/docs/posts/page/3/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/page/4/index.html b/docs/posts/page/4/index.html index bf6010f00..bcae6a634 100644 --- a/docs/posts/page/4/index.html +++ b/docs/posts/page/4/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/page/5/index.html b/docs/posts/page/5/index.html index 89773c1fb..a311235fb 100644 --- a/docs/posts/page/5/index.html +++ b/docs/posts/page/5/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/page/6/index.html b/docs/posts/page/6/index.html index cfa8a8c99..416bf9e64 100644 --- a/docs/posts/page/6/index.html +++ b/docs/posts/page/6/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/page/7/index.html b/docs/posts/page/7/index.html index cefc3ee7e..cde988a15 100644 --- a/docs/posts/page/7/index.html +++ b/docs/posts/page/7/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/posts/page/8/index.html b/docs/posts/page/8/index.html index 1796c2111..bb57c4b20 100644 --- a/docs/posts/page/8/index.html +++ b/docs/posts/page/8/index.html @@ -10,14 +10,14 @@ - + - + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 6d1f9620c..113ea5051 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -3,19 +3,19 @@ xmlns:xhtml="http://www.w3.org/1999/xhtml"> https://alanorth.github.io/cgspace-notes/categories/ - 2021-06-16T18:31:15+03:00 + 2021-06-17T18:16:18+03:00 https://alanorth.github.io/cgspace-notes/ - 2021-06-16T18:31:15+03:00 + 2021-06-17T18:16:18+03:00 https://alanorth.github.io/cgspace-notes/2021-06/ - 2021-06-16T18:31:15+03:00 + 2021-06-17T18:16:18+03:00 https://alanorth.github.io/cgspace-notes/categories/notes/ - 2021-06-16T18:31:15+03:00 + 2021-06-17T18:16:18+03:00 https://alanorth.github.io/cgspace-notes/posts/ - 2021-06-16T18:31:15+03:00 + 2021-06-17T18:16:18+03:00 https://alanorth.github.io/cgspace-notes/2021-05/ 2021-05-30T22:09:06+03:00 diff --git a/docs/tags/index.html b/docs/tags/index.html index c1e7cf19d..4d644508d 100644 --- a/docs/tags/index.html +++ b/docs/tags/index.html @@ -17,7 +17,7 @@ - + diff --git a/docs/tags/migration/index.html b/docs/tags/migration/index.html index 4d430cb3f..3a963a57f 100644 --- a/docs/tags/migration/index.html +++ b/docs/tags/migration/index.html @@ -17,7 +17,7 @@ - + diff --git a/docs/tags/notes/index.html b/docs/tags/notes/index.html index a4b08eb9d..613a5d698 100644 --- a/docs/tags/notes/index.html +++ b/docs/tags/notes/index.html @@ -17,7 +17,7 @@ - + diff --git a/docs/tags/notes/page/2/index.html b/docs/tags/notes/page/2/index.html index 41866efb7..32120f4ce 100644 --- a/docs/tags/notes/page/2/index.html +++ b/docs/tags/notes/page/2/index.html @@ -17,7 +17,7 @@ - + diff --git a/docs/tags/notes/page/3/index.html b/docs/tags/notes/page/3/index.html index 9e199ab4c..49f1d653b 100644 --- a/docs/tags/notes/page/3/index.html +++ b/docs/tags/notes/page/3/index.html @@ -17,7 +17,7 @@ - +