From 26f17edd927be05bf3fcb3c240eb78338fd82509 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Sun, 22 Nov 2020 23:08:49 +0200 Subject: [PATCH] Add notes for 2020-11-22 --- content/posts/2020-11.md | 50 ++++++++++++++++ content/posts/cgspace-dspace6-upgrade.md | 8 ++- 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 | 61 ++++++++++++++++++-- docs/2020/11/postgres_locks_ALL-week3.png | Bin 0 -> 12684 bytes docs/2020/11/postgres_xlog-week2.png | Bin 0 -> 7862 bytes 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 | 10 ++-- 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/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/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 +- static/2020/11/postgres_locks_ALL-week3.png | Bin 0 -> 12684 bytes static/2020/11/postgres_xlog-week2.png | Bin 0 -> 7862 bytes 97 files changed, 232 insertions(+), 123 deletions(-) create mode 100644 docs/2020/11/postgres_locks_ALL-week3.png create mode 100644 docs/2020/11/postgres_xlog-week2.png create mode 100644 static/2020/11/postgres_locks_ALL-week3.png create mode 100644 static/2020/11/postgres_xlog-week2.png diff --git a/content/posts/2020-11.md b/content/posts/2020-11.md index e8deb5ad2..f6f9a3dc6 100644 --- a/content/posts/2020-11.md +++ b/content/posts/2020-11.md @@ -409,4 +409,54 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = - Very curious that there was such a high number of rolled back transactions after the update +## 2020-11-22 + +- PostgreSQL situation on CGSpace (linode18) looks much better now: + +![PostgreSQL locks week](/cgspace-notes/2020/11/postgres_locks_ALL-week3.png) +![PostgreSQL transaction log week](/cgspace-notes/2020/11/postgres_xlog-week2.png) + +- In other news, I noticed that harvesting DSpace 6 works fine in OpenRXV, but the statistics fail on page 1 + - I filed an issue: https://github.com/ilri/OpenRXV/issues/59 +- Abenet asked for help trying to add a new user to the Bioversity and CIAT groups on CGSpace + - I see that the user search is split on five results, so the user in question appears on page 2 + - I asked Abenet if she was getting an error or it was simply this... +- Maria Garuccio sent me an example report that she wants to be able to generate from AReS + - First, she would like to have the option to group by output type + - Second, she would like to be able to control the sorting in the template, like sorting the citation alphabetically + - I filed an issue: https://github.com/ilri/OpenRXV/issues/60 +- Mohammad Salem had asked if there was an item ID to UUID mapping for CGSpace + - I found a thread on the dspace-tech mailing list that pointed out that there is a new `uuid` column in the item table + - Only old items have an `item_id` so we can get a mapping easily: + +``` +dspace=# \COPY (SELECT item_id,uuid FROM item WHERE in_archive='t' AND withdrawn='f' AND item_id IS NOT NULL) TO /tmp/2020-11-22-item-id2uuid.csv WITH CSV HEADER; +COPY 87411 +``` + +- Saving some notes I wrote down about faceting by community and collection in Solr, for potential use in the future in the DSpace Statistics API +- Facet by owningComm to see total number of distinct communities (136): + +``` + facet=true&facet.mincount=1&facet.field=owningComm&facet.limit=1&facet.offset=0&stats=true&stats.field=id&stats.calcdistinct=true +``` + +- Facet by owningComm and get the first 5 distinct: + +``` + facet=true&facet.mincount=1&facet.field=owningComm&facet.limit=5&facet.offset=0&facet.pivot=id,countryCode +``` + +- Facet by owningComm and countryCode using facet.pivot and maybe I can just skip the normal facet params? + +``` +facet=true&f.owningComm.facet.limit=5&f.owningComm.facet.offset=5&facet.pivot=owningComm,countryCode +``` + +- Facet by owningComm and countryCode using facet.pivot and limiting to top five countries... fuck it's possible! + +``` +facet=true&f.owningComm.facet.limit=5&f.owningComm.facet.offset=5&f.countryCode.facet.limit=5&facet.pivot=owningComm,countryCode +``` + diff --git a/content/posts/cgspace-dspace6-upgrade.md b/content/posts/cgspace-dspace6-upgrade.md index 3ab523a37..960794011 100644 --- a/content/posts/cgspace-dspace6-upgrade.md +++ b/content/posts/cgspace-dspace6-upgrade.md @@ -410,8 +410,14 @@ $ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H ### Processing Solr statistics with AtomicStatisticsUpdateCLI -On 2020-11-18 I finished processing the Solr statistics with solr-upgrade-statistics-6x and I started processing them with AtomicStatisticsUpdateCLI: +On 2020-11-18 I finished processing the Solr statistics with solr-upgrade-statistics-6x and I started processing them with AtomicStatisticsUpdateCLI. + +## statistics + +First the current year's statistics core, in 12-hour batches: ``` $ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics ``` + +It took ~38 hours to finish processing this core. diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index 5356f2e83..837543929 100644 --- a/docs/2015-11/index.html +++ b/docs/2015-11/index.html @@ -31,7 +31,7 @@ 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 aaf5ebc5e..5e85ae1ce 100644 --- a/docs/2015-12/index.html +++ b/docs/2015-12/index.html @@ -33,7 +33,7 @@ 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 d18a61197..92630ce08 100644 --- a/docs/2016-01/index.html +++ b/docs/2016-01/index.html @@ -25,7 +25,7 @@ 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 b53816233..ea5a9f763 100644 --- a/docs/2016-02/index.html +++ b/docs/2016-02/index.html @@ -35,7 +35,7 @@ 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 46cde74a2..d5c226505 100644 --- a/docs/2016-03/index.html +++ b/docs/2016-03/index.html @@ -25,7 +25,7 @@ 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 09859e9af..121425e27 100644 --- a/docs/2016-04/index.html +++ b/docs/2016-04/index.html @@ -29,7 +29,7 @@ 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 3d02eb5a6..72e439d6b 100644 --- a/docs/2016-05/index.html +++ b/docs/2016-05/index.html @@ -31,7 +31,7 @@ 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 9cafeda62..94b237e6a 100644 --- a/docs/2016-06/index.html +++ b/docs/2016-06/index.html @@ -31,7 +31,7 @@ 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 44a978fc0..8fae2dd74 100644 --- a/docs/2016-07/index.html +++ b/docs/2016-07/index.html @@ -41,7 +41,7 @@ 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 a2020ec40..bf1f2e0c3 100644 --- a/docs/2016-08/index.html +++ b/docs/2016-08/index.html @@ -39,7 +39,7 @@ $ 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 a4e062c7c..d02188cd3 100644 --- a/docs/2016-09/index.html +++ b/docs/2016-09/index.html @@ -31,7 +31,7 @@ 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 4e93429e7..ab456a1c1 100644 --- a/docs/2016-10/index.html +++ b/docs/2016-10/index.html @@ -39,7 +39,7 @@ 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 61f44f64f..76d135efa 100644 --- a/docs/2016-11/index.html +++ b/docs/2016-11/index.html @@ -23,7 +23,7 @@ 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 6e3578e53..50797c5ac 100644 --- a/docs/2016-12/index.html +++ b/docs/2016-12/index.html @@ -43,7 +43,7 @@ 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 6ff69a639..fed592875 100644 --- a/docs/2017-01/index.html +++ b/docs/2017-01/index.html @@ -25,7 +25,7 @@ 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 5aadcd0ee..f8e617d26 100644 --- a/docs/2017-02/index.html +++ b/docs/2017-02/index.html @@ -47,7 +47,7 @@ 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 7adbb390f..7e453dfaf 100644 --- a/docs/2017-03/index.html +++ b/docs/2017-03/index.html @@ -51,7 +51,7 @@ 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 2867e54be..5d308bccd 100644 --- a/docs/2017-04/index.html +++ b/docs/2017-04/index.html @@ -37,7 +37,7 @@ 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 d7edd13af..4d4b33a09 100644 --- a/docs/2017-05/index.html +++ b/docs/2017-05/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/2017-06/index.html b/docs/2017-06/index.html index 2587beb47..f509e4864 100644 --- a/docs/2017-06/index.html +++ b/docs/2017-06/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/2017-07/index.html b/docs/2017-07/index.html index 1f593ae0b..16190c761 100644 --- a/docs/2017-07/index.html +++ b/docs/2017-07/index.html @@ -33,7 +33,7 @@ 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 823e24195..6ee89ad2b 100644 --- a/docs/2017-08/index.html +++ b/docs/2017-08/index.html @@ -57,7 +57,7 @@ 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 7ead7e7cd..e7f7f9047 100644 --- a/docs/2017-09/index.html +++ b/docs/2017-09/index.html @@ -29,7 +29,7 @@ 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 0f38d0ab7..e03e370a2 100644 --- a/docs/2017-10/index.html +++ b/docs/2017-10/index.html @@ -31,7 +31,7 @@ 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 8a5e0353b..481f96ddd 100644 --- a/docs/2017-11/index.html +++ b/docs/2017-11/index.html @@ -45,7 +45,7 @@ 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 c8d8ebc53..46e487855 100644 --- a/docs/2017-12/index.html +++ b/docs/2017-12/index.html @@ -27,7 +27,7 @@ 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 26799a768..629bf65d4 100644 --- a/docs/2018-01/index.html +++ b/docs/2018-01/index.html @@ -147,7 +147,7 @@ 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 031d847f3..484215dc5 100644 --- a/docs/2018-02/index.html +++ b/docs/2018-02/index.html @@ -27,7 +27,7 @@ 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 8add149f7..5d184bf78 100644 --- a/docs/2018-03/index.html +++ b/docs/2018-03/index.html @@ -21,7 +21,7 @@ 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 0acdfd4e8..0d6ef501c 100644 --- a/docs/2018-04/index.html +++ b/docs/2018-04/index.html @@ -23,7 +23,7 @@ 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 539a58a63..0b8a8f0cf 100644 --- a/docs/2018-05/index.html +++ b/docs/2018-05/index.html @@ -35,7 +35,7 @@ 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 791c6e003..1f65076fe 100644 --- a/docs/2018-06/index.html +++ b/docs/2018-06/index.html @@ -55,7 +55,7 @@ real 74m42.646s user 8m5.056s sys 2m7.289s "/> - + diff --git a/docs/2018-07/index.html b/docs/2018-07/index.html index a81e19e5c..970673a7d 100644 --- a/docs/2018-07/index.html +++ b/docs/2018-07/index.html @@ -33,7 +33,7 @@ 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 58c4eeb48..4d78268ab 100644 --- a/docs/2018-08/index.html +++ b/docs/2018-08/index.html @@ -43,7 +43,7 @@ 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 64de6604f..2ea8f9cca 100644 --- a/docs/2018-09/index.html +++ b/docs/2018-09/index.html @@ -27,7 +27,7 @@ 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 e925ddf1d..b5bea1842 100644 --- a/docs/2018-10/index.html +++ b/docs/2018-10/index.html @@ -23,7 +23,7 @@ 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 17079de46..71b144476 100644 --- a/docs/2018-11/index.html +++ b/docs/2018-11/index.html @@ -33,7 +33,7 @@ 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 19dac4158..a62b24509 100644 --- a/docs/2018-12/index.html +++ b/docs/2018-12/index.html @@ -33,7 +33,7 @@ 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 3fa516909..cd83e2581 100644 --- a/docs/2019-01/index.html +++ b/docs/2019-01/index.html @@ -47,7 +47,7 @@ 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 dd3763821..08c523ca1 100644 --- a/docs/2019-02/index.html +++ b/docs/2019-02/index.html @@ -69,7 +69,7 @@ real 0m19.873s user 0m22.203s sys 0m1.979s "/> - + diff --git a/docs/2019-03/index.html b/docs/2019-03/index.html index 529a4ed66..b5559a3eb 100644 --- a/docs/2019-03/index.html +++ b/docs/2019-03/index.html @@ -43,7 +43,7 @@ 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 2c9e3889e..d374485a8 100644 --- a/docs/2019-04/index.html +++ b/docs/2019-04/index.html @@ -61,7 +61,7 @@ $ ./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 49b37b265..b3419222d 100644 --- a/docs/2019-05/index.html +++ b/docs/2019-05/index.html @@ -45,7 +45,7 @@ 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 08c8d324c..db51accb1 100644 --- a/docs/2019-06/index.html +++ b/docs/2019-06/index.html @@ -31,7 +31,7 @@ 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 fd5b53b0e..729f78758 100644 --- a/docs/2019-07/index.html +++ b/docs/2019-07/index.html @@ -35,7 +35,7 @@ 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 3c595fe80..95f299c7f 100644 --- a/docs/2019-08/index.html +++ b/docs/2019-08/index.html @@ -43,7 +43,7 @@ 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 32ecac81c..9da373b4d 100644 --- a/docs/2019-09/index.html +++ b/docs/2019-09/index.html @@ -69,7 +69,7 @@ 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 08b88af06..e789845ae 100644 --- a/docs/2019-10/index.html +++ b/docs/2019-10/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/2019-11/index.html b/docs/2019-11/index.html index de9908735..ca996db2b 100644 --- a/docs/2019-11/index.html +++ b/docs/2019-11/index.html @@ -55,7 +55,7 @@ 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 8c254b889..64514df7f 100644 --- a/docs/2019-12/index.html +++ b/docs/2019-12/index.html @@ -43,7 +43,7 @@ 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 7c9fbb249..88e9cc74b 100644 --- a/docs/2020-01/index.html +++ b/docs/2020-01/index.html @@ -53,7 +53,7 @@ I tweeted the CGSpace repository link "/> - + diff --git a/docs/2020-02/index.html b/docs/2020-02/index.html index 42a696d64..5c0e5b45e 100644 --- a/docs/2020-02/index.html +++ b/docs/2020-02/index.html @@ -35,7 +35,7 @@ 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 e150b8488..e73cb87b7 100644 --- a/docs/2020-03/index.html +++ b/docs/2020-03/index.html @@ -39,7 +39,7 @@ 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 2400cddea..540820e53 100644 --- a/docs/2020-04/index.html +++ b/docs/2020-04/index.html @@ -45,7 +45,7 @@ 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 ec6d6c1c9..7e8b0d287 100644 --- a/docs/2020-05/index.html +++ b/docs/2020-05/index.html @@ -31,7 +31,7 @@ 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 9d7e525ee..c2554b151 100644 --- a/docs/2020-06/index.html +++ b/docs/2020-06/index.html @@ -33,7 +33,7 @@ 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 ff408aef3..51949d6c8 100644 --- a/docs/2020-07/index.html +++ b/docs/2020-07/index.html @@ -35,7 +35,7 @@ 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 277687b8f..0d345f432 100644 --- a/docs/2020-08/index.html +++ b/docs/2020-08/index.html @@ -33,7 +33,7 @@ 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 ef40fcb17..57f8cd7e5 100644 --- a/docs/2020-09/index.html +++ b/docs/2020-09/index.html @@ -45,7 +45,7 @@ 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 2dcc1fe89..5dc34a2ac 100644 --- a/docs/2020-10/index.html +++ b/docs/2020-10/index.html @@ -41,7 +41,7 @@ During the FlywayDB migration I got an error: "/> - + diff --git a/docs/2020-11/index.html b/docs/2020-11/index.html index a616fdd8a..00789f3f1 100644 --- a/docs/2020-11/index.html +++ b/docs/2020-11/index.html @@ -17,7 +17,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat - + @@ -29,7 +29,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat "/> - + @@ -39,9 +39,9 @@ So far we’ve spent at least fifty hours to process the statistics and stat "@type": "BlogPosting", "headline": "November, 2020", "url": "https://alanorth.github.io/cgspace-notes/2020-11/", - "wordCount": "2743", + "wordCount": "3039", "datePublished": "2020-11-01T13:11:54+02:00", - "dateModified": "2020-11-19T22:40:48+02:00", + "dateModified": "2020-11-19T22:41:55+02:00", "author": { "@type": "Person", "name": "Alan Orth" @@ -568,7 +568,58 @@ org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error whil - +

2020-11-22

+ +

PostgreSQL locks week +PostgreSQL transaction log week

+ +
dspace=# \COPY (SELECT item_id,uuid FROM item WHERE in_archive='t' AND withdrawn='f' AND item_id IS NOT NULL) TO /tmp/2020-11-22-item-id2uuid.csv WITH CSV HEADER;
+COPY 87411
+
+
  facet=true&facet.mincount=1&facet.field=owningComm&facet.limit=1&facet.offset=0&stats=true&stats.field=id&stats.calcdistinct=true
+
+
  facet=true&facet.mincount=1&facet.field=owningComm&facet.limit=5&facet.offset=0&facet.pivot=id,countryCode
+
+
facet=true&f.owningComm.facet.limit=5&f.owningComm.facet.offset=5&facet.pivot=owningComm,countryCode
+
+
facet=true&f.owningComm.facet.limit=5&f.owningComm.facet.offset=5&f.countryCode.facet.limit=5&facet.pivot=owningComm,countryCode
+
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b/docs/categories/notes/page/2/index.html index c11b0ea7a..5d3551bb7 100644 --- a/docs/categories/notes/page/2/index.html +++ b/docs/categories/notes/page/2/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/categories/notes/page/3/index.html b/docs/categories/notes/page/3/index.html index a81ae84fb..231fbdb35 100644 --- a/docs/categories/notes/page/3/index.html +++ b/docs/categories/notes/page/3/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/categories/notes/page/4/index.html b/docs/categories/notes/page/4/index.html index e6ece4165..a15041f25 100644 --- a/docs/categories/notes/page/4/index.html +++ b/docs/categories/notes/page/4/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/categories/notes/page/5/index.html b/docs/categories/notes/page/5/index.html index a643509ea..f69e45e3c 100644 --- a/docs/categories/notes/page/5/index.html +++ b/docs/categories/notes/page/5/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/cgiar-library-migration/index.html b/docs/cgiar-library-migration/index.html index 7d347a871..85d92809c 100644 --- a/docs/cgiar-library-migration/index.html +++ b/docs/cgiar-library-migration/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/cgspace-cgcorev2-migration/index.html b/docs/cgspace-cgcorev2-migration/index.html index 7e6abf595..c9a24c663 100644 --- a/docs/cgspace-cgcorev2-migration/index.html +++ b/docs/cgspace-cgcorev2-migration/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/cgspace-dspace6-upgrade/index.html b/docs/cgspace-dspace6-upgrade/index.html index ec191ea3c..d9af41078 100644 --- a/docs/cgspace-dspace6-upgrade/index.html +++ b/docs/cgspace-dspace6-upgrade/index.html @@ -15,7 +15,7 @@ - + @@ -25,7 +25,7 @@ "@type": "BlogPosting", "headline": "CGSpace DSpace 6 Upgrade", "url": "https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/", - "wordCount": "1281", + "wordCount": "1300", "datePublished": "2020-11-15T13:27:35+02:00", "dateModified": "2020-11-18T23:15:06+02:00", "author": { @@ -403,9 +403,11 @@ $ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018 
$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"

Processing Solr statistics with AtomicStatisticsUpdateCLI

-

On 2020-11-18 I finished processing the Solr statistics with solr-upgrade-statistics-6x and I started processing them with AtomicStatisticsUpdateCLI:

+

On 2020-11-18 I finished processing the Solr statistics with solr-upgrade-statistics-6x and I started processing them with AtomicStatisticsUpdateCLI.

+

statistics

+

First the current year’s statistics core, in 12-hour batches:

$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics
-
+

It took ~38 hours to finish processing this core.

diff --git a/docs/index.html b/docs/index.html index 0b3d6bd9d..94c4ddc2a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/page/2/index.html b/docs/page/2/index.html index 8058d4c9e..8eb5e95c5 100644 --- a/docs/page/2/index.html +++ b/docs/page/2/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/page/3/index.html b/docs/page/3/index.html index b148d0f04..f3b9a2f66 100644 --- a/docs/page/3/index.html +++ b/docs/page/3/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/page/4/index.html b/docs/page/4/index.html index 9edff9be3..3396d2110 100644 --- a/docs/page/4/index.html +++ b/docs/page/4/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/page/5/index.html b/docs/page/5/index.html index 1fe500d8b..f428c3f8e 100644 --- a/docs/page/5/index.html +++ b/docs/page/5/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/page/6/index.html b/docs/page/6/index.html index bd77e36d2..b32f3f365 100644 --- a/docs/page/6/index.html +++ b/docs/page/6/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/page/7/index.html b/docs/page/7/index.html index 0f4a5fc31..5016784ef 100644 --- a/docs/page/7/index.html +++ b/docs/page/7/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/posts/index.html b/docs/posts/index.html index 45718ad40..2d3e2b36e 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/posts/page/2/index.html b/docs/posts/page/2/index.html index 48aafc5f6..1d4b39115 100644 --- a/docs/posts/page/2/index.html +++ b/docs/posts/page/2/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/posts/page/3/index.html b/docs/posts/page/3/index.html index ab344ddbe..6d85cdd4d 100644 --- a/docs/posts/page/3/index.html +++ b/docs/posts/page/3/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/posts/page/4/index.html b/docs/posts/page/4/index.html index 8e5faa9df..626e59bc2 100644 --- a/docs/posts/page/4/index.html +++ b/docs/posts/page/4/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/posts/page/5/index.html b/docs/posts/page/5/index.html index 550503a00..543521c4c 100644 --- a/docs/posts/page/5/index.html +++ b/docs/posts/page/5/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/posts/page/6/index.html b/docs/posts/page/6/index.html index 28cac2ec8..02941f7e8 100644 --- a/docs/posts/page/6/index.html +++ b/docs/posts/page/6/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/posts/page/7/index.html b/docs/posts/page/7/index.html index dc626f507..5693424a7 100644 --- a/docs/posts/page/7/index.html +++ b/docs/posts/page/7/index.html @@ -9,12 +9,12 @@ - + - + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index fb4637186..b21113c24 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,7 +4,7 @@ https://alanorth.github.io/cgspace-notes/categories/ - 2020-11-19T22:40:48+02:00 + 2020-11-19T22:41:55+02:00 @@ -14,7 +14,7 @@ https://alanorth.github.io/cgspace-notes/ - 2020-11-19T22:40:48+02:00 + 2020-11-19T22:41:55+02:00 @@ -24,12 +24,12 @@ https://alanorth.github.io/cgspace-notes/categories/notes/ - 2020-11-19T22:40:48+02:00 + 2020-11-19T22:41:55+02:00 https://alanorth.github.io/cgspace-notes/posts/ - 2020-11-19T22:40:48+02:00 + 2020-11-19T22:41:55+02:00 @@ -39,7 +39,7 @@ https://alanorth.github.io/cgspace-notes/2020-11/ - 2020-11-19T22:40:48+02:00 + 2020-11-19T22:41:55+02:00 diff --git a/docs/tags/index.html b/docs/tags/index.html index 29482966c..ab8a218e0 100644 --- a/docs/tags/index.html +++ b/docs/tags/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/migration/index.html b/docs/tags/migration/index.html index 51a69fe92..c8777119e 100644 --- a/docs/tags/migration/index.html +++ b/docs/tags/migration/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/notes/index.html b/docs/tags/notes/index.html index 5267749a3..fc44a1a0d 100644 --- a/docs/tags/notes/index.html +++ b/docs/tags/notes/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/notes/page/2/index.html 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