From c00e6395d8771d2efec5613ea85f6c35ab47d003 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Thu, 1 Jul 2021 08:53:21 +0300 Subject: [PATCH] Notes for 2021-06-30 --- content/posts/2021-06.md | 34 ++++++++++++++++++ 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 | 40 +++++++++++++++++++--- 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/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/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/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 +- 101 files changed, 195 insertions(+), 129 deletions(-) diff --git a/content/posts/2021-06.md b/content/posts/2021-06.md index 5b46fe43d..00421e018 100644 --- a/content/posts/2021-06.md +++ b/content/posts/2021-06.md @@ -461,5 +461,39 @@ dspace.log.2021-06-27 - He said they had to do the same thing that they did last time: switch to the postgres user and kill all activity - He said they found tons of connections to the REST API, like 3-4 per second, and asked if that was normal - I pointed him to our Tomcat server.xml configuration, saying that we purposefully isolated the Tomcat connection pools between the API and XMLUI for this purpose... +- Export a list of all CGSpace's AGROVOC keywords with counts for Enrico and Elizabeth Arnaud to discuss with AGROVOC: + +```console +localhost/dspace63= > \COPY (SELECT DISTINCT text_value AS "dcterms.subject", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 187 GROUP BY "dcterms.subject" ORDER BY count DESC) to /tmp/2021-06-30-agrovoc.csv WITH CSV HEADER; +COPY 20780 +``` + +- Actually Enrico wanted NON AGROVOC, so I extracted all the center and CRP subjects (ignoring system office and themes): + +```console +localhost/dspace63= > \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242) GROUP BY subject ORDER BY count DESC) to /tmp/2021-06-30-non-agrovoc.csv WITH CSV HEADER; +COPY 1710 +``` + +- Fix an issue in the Ansible infrastructure playbooks for the DSpace role + - It was causing the template module to fail when setting up the npm environment + - We needed to install `acl` so that Ansible can use `setfacl` on the target file before becoming an unprivileged user +- I saw a strange message in the Tomcat 7 journal on DSpace Test (linode26): + +```console +Jun 30 16:00:09 linode26 tomcat7[30294]: WARNING: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [111,733] milliseconds. +``` + +- What's even crazier is that it is twice that on CGSpace (linode18)! +- Apparently OpenJDK defaults to using `/dev/random` (see `/etc/java-8-openjdk/security/java.security`): + +```console +securerandom.source=file:/dev/urandom +``` + +- `/dev/random` blocks and can take a long time to get entropy, and urandom on modern Linux is a cryptographically secure pseudorandom number generator + - Now Tomcat starts much faster and no warning is printed so I'm going to add this to our Ansible infrastructure playbooks +- Interesting resource about the lore behind the `/dev/./urandom` workaround that is posted all over the Internet, apparently due to a bug in early JVMs: https://bugs.java.com/bugdatabase/view_bug.do?bug_id=6202721 +- I'm experimenting with using PgBouncer for pooling instead of Tomcat's JDBC diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index be4c954fe..982a4257c 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 7491daf59..fc3c7ab3e 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 a87177a1a..ed6ac2ecb 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 7413104be..afffd7079 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 ab0c5d098..6c7af09b1 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 cac3a0a73..ab0e7b849 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 dd8e8cbc7..7d5d4343d 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 68e75454c..d0bee0989 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 74fa079de..d92275c35 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 12abc6c90..a3cb33c81 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 bded9bd6b..e75015c99 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 83ca10c2e..3a3023400 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 e690e3e5c..bc5f36df3 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 0cbd5baea..90a778f10 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 9ca148834..2c218fa57 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 0a5318c62..529cab73f 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 da6bd293b..f3afd852e 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 46ff9da0b..77e0b3660 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 a99dc3f9a..ad99adfba 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 9ada8f265..11a5f8883 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 a4a2ce50e..749fd04f6 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 ebbbf14d2..5a32b6673 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 b51826839..fd6fe755c 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 7eb1ec3a9..4d5fd1623 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 84a4610d3..2c66ec310 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 63a8ebac8..38a9dbf65 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 59b58b894..2ae8a7b62 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 92c5d7998..b4068c12d 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 7bca8564c..78d0a52de 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 158ebb1eb..6f59a586b 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 925af2df5..191e695a4 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 fa04d31f1..53d8a48ae 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 882983e15..7b97a955e 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 444f823dd..ae6a4e16d 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 f195f9faa..bd8d0da31 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 080f77461..da4dc3910 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 ddb17f009..274272f69 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 bf80468a1..8aae7a3a5 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 174189da6..6f6d1ddfe 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 3600194b5..c63cf7abc 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 906ff6904..767b98728 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 02dec916c..050aee3e2 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 3fff039f6..168b3e71d 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 a804e5668..7231c2d5a 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 e18aa7e10..d13817f52 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 ed9f25894..db91c749a 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 fb7b093de..11fe1abd3 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 e7062f6e2..230b346aa 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 f07418ddd..15dedcd9d 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 59b7da3c4..6a0463cbf 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 dca57611e..45744f6d3 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 265706ab5..5a796641d 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 e07f2cb0c..6568c8411 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 e1cf80ade..d04270d36 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 fd7246e67..dbdd5cb65 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 26909dc20..1254d317b 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 8231f0e59..a362d436d 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 53f6ac8a3..7d68dd846 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 7f4f9e5d4..6a2416a83 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 4df483181..d27131df5 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: "/> - + diff --git a/docs/2020-11/index.html b/docs/2020-11/index.html index e7bb70b0e..94e9e1d4d 100644 --- a/docs/2020-11/index.html +++ b/docs/2020-11/index.html @@ -32,7 +32,7 @@ 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 e2163d487..a4b83cd2b 100644 --- a/docs/2020-12/index.html +++ b/docs/2020-12/index.html @@ -36,7 +36,7 @@ I started processing those (about 411,000 records): "/> - + diff --git a/docs/2021-01/index.html b/docs/2021-01/index.html index 048d1a6f0..32d476521 100644 --- a/docs/2021-01/index.html +++ b/docs/2021-01/index.html @@ -50,7 +50,7 @@ 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 62f6e1234..26346564f 100644 --- a/docs/2021-02/index.html +++ b/docs/2021-02/index.html @@ -60,7 +60,7 @@ $ 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 fa1961a81..53a48bd9b 100644 --- a/docs/2021-03/index.html +++ b/docs/2021-03/index.html @@ -34,7 +34,7 @@ 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 f06fc2f45..866bed0ee 100644 --- a/docs/2021-04/index.html +++ b/docs/2021-04/index.html @@ -44,7 +44,7 @@ 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 ed7da6360..799dc4580 100644 --- a/docs/2021-05/index.html +++ b/docs/2021-05/index.html @@ -36,7 +36,7 @@ I looked at the top user agents and IPs in the Solr statistics for last month an I will add the RI/1.0 pattern to our DSpace agents overload and purge them from Solr (we had previously seen this agent with 9,000 hits or so in 2020-09), but I think I will leave the Microsoft Word one… as that’s an actual user… "/> - + diff --git a/docs/2021-06/index.html b/docs/2021-06/index.html index cba9c41ba..64aab24f9 100644 --- a/docs/2021-06/index.html +++ b/docs/2021-06/index.html @@ -20,7 +20,7 @@ I simply started it and AReS was running again: - + @@ -36,7 +36,7 @@ I simply started it and AReS was running again: "/> - + @@ -46,9 +46,9 @@ I simply started it and AReS was running again: "@type": "BlogPosting", "headline": "June, 2021", "url": "https://alanorth.github.io/cgspace-notes/2021-06/", - "wordCount": "3202", + "wordCount": "3505", "datePublished": "2021-06-01T10:51:07+03:00", - "dateModified": "2021-06-27T20:35:32+03:00", + "dateModified": "2021-06-30T12:21:16+03:00", "author": { "@type": "Person", "name": "Alan Orth" @@ -639,6 +639,38 @@ dspace.log.2021-06-27
  • I pointed him to our Tomcat server.xml configuration, saying that we purposefully isolated the Tomcat connection pools between the API and XMLUI for this purpose…
    • +
  • Export a list of all CGSpace’s AGROVOC keywords with counts for Enrico and Elizabeth Arnaud to discuss with AGROVOC:
    • + +
    localhost/dspace63= > \COPY (SELECT DISTINCT text_value AS "dcterms.subject", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 187 GROUP BY "dcterms.subject" ORDER BY count DESC) to /tmp/2021-06-30-agrovoc.csv WITH CSV HEADER;
+COPY 20780
+
    +
    localhost/dspace63= > \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242) GROUP BY subject ORDER BY count DESC) to /tmp/2021-06-30-non-agrovoc.csv WITH CSV HEADER;
+COPY 1710
+
    +
    Jun 30 16:00:09 linode26 tomcat7[30294]: WARNING: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [111,733] milliseconds.
+
    +
    securerandom.source=file:/dev/urandom
+
    diff --git a/docs/404.html b/docs/404.html index 6b5d27df8..eb748ef8f 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 01da73d2c..6eae87254 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 ba07a94f3..f912488b4 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 c85d61a79..6afc89dbe 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 afaf72d99..ea38ad41d 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 7becc77a4..b2ac38635 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 63cbaa193..1d14d96b1 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 80432852a..0509bdca6 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 e0343a2f9..f42b5d130 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 ee6aca9c1..a3b785134 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 edd465ac9..8028d23b9 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 7efcda407..d1524d7ab 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 c89b450be..22cf4ef25 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 4f99fb671..c532b6dd5 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 88b94bd3d..06241034d 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 5acd0ac7b..8a41898c6 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 cd06d6f58..f41a5a65e 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 40edd6578..787594b29 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 9df9b5e7f..29bcdeae1 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 b8a34188a..d6e971d32 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 8709de8e2..c261a2738 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 cfa40f22b..d6d3708f0 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 978ab3d11..c6a5436a8 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 5026f4145..ce6db24bc 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 6e2229ae2..b01a2ce15 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 aa15741a3..933cf41cc 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 84454acee..92a5e1f3a 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/ - 2021-06-27T20:35:32+03:00 + 2021-06-30T12:21:16+03:00 https://alanorth.github.io/cgspace-notes/ - 2021-06-27T20:35:32+03:00 + 2021-06-30T12:21:16+03:00 https://alanorth.github.io/cgspace-notes/2021-06/ - 2021-06-27T20:35:32+03:00 + 2021-06-30T12:21:16+03:00 https://alanorth.github.io/cgspace-notes/categories/notes/ - 2021-06-27T20:35:32+03:00 + 2021-06-30T12:21:16+03:00 https://alanorth.github.io/cgspace-notes/posts/ - 2021-06-27T20:35:32+03:00 + 2021-06-30T12:21:16+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 2a2d251ff..5cd645ae2 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 8aa0ce2c5..b94ef9edf 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 de41855e9..70cef10f0 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 c049d16b9..60646ecf5 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 294f105aa..9261c70ce 100644 --- a/docs/tags/notes/page/3/index.html +++ b/docs/tags/notes/page/3/index.html @@ -17,7 +17,7 @@ - +