From 2a36e6f5d4133e84385c3e9ae9283ac17b1e2e25 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Thu, 26 Mar 2020 15:14:14 +0200 Subject: [PATCH] Add notes for 2020-03-26 --- content/posts/2020-03.md | 36 +++++++++++++++++++ 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 | 42 +++++++++++++++++++--- docs/404.html | 2 +- docs/categories/index.html | 2 +- docs/categories/notes/index.html | 2 +- docs/categories/notes/page/2/index.html | 2 +- docs/categories/notes/page/3/index.html | 2 +- docs/categories/notes/page/4/index.html | 2 +- docs/categories/page/2/index.html | 2 +- docs/categories/page/3/index.html | 2 +- docs/categories/page/4/index.html | 2 +- docs/categories/page/5/index.html | 2 +- docs/categories/page/6/index.html | 2 +- docs/cgiar-library-migration/index.html | 2 +- docs/cgspace-cgcorev2-migration/index.html | 2 +- docs/index.html | 2 +- docs/page/2/index.html | 2 +- docs/page/3/index.html | 2 +- docs/page/4/index.html | 2 +- docs/page/5/index.html | 2 +- docs/page/6/index.html | 2 +- docs/posts/index.html | 2 +- docs/posts/page/2/index.html | 2 +- docs/posts/page/3/index.html | 2 +- docs/posts/page/4/index.html | 2 +- docs/posts/page/5/index.html | 2 +- docs/posts/page/6/index.html | 2 +- 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 +- docs/tags/page/2/index.html | 2 +- docs/tags/page/3/index.html | 2 +- docs/tags/page/4/index.html | 2 +- docs/tags/page/5/index.html | 2 +- docs/tags/page/6/index.html | 2 +- 90 files changed, 166 insertions(+), 96 deletions(-) diff --git a/content/posts/2020-03.md b/content/posts/2020-03.md index f120b240d..92110de38 100644 --- a/content/posts/2020-03.md +++ b/content/posts/2020-03.md @@ -278,4 +278,40 @@ $ lein run /tmp/affiliations.csv name id - I sent Atmire a message to ask if they managed to start working on the DSpace 6 port, as the last communication was twenty-six days ago when they said they were going to secure technical resources to do so - Start adapting the `dspace` role in our [Ansible infrastructure playbooks](https://github.com/ilri/rmg-ansible-public) for DSpace 6 support +## 2020-03-26 + +- More work adapting the `dspace` role in our Ansible infrastructure scripts to DSpace 6 +- Update Tomcat to version 7.0.103 in the Ansible infrastrcutrue playbooks and deploy on DSpace Test (linode26) +- Maria sent me a few new ORCID identifiers from Bioversity so I combined them with our existing ones, filtered the unique ones, and then resolved their names using my `resolve-orcids.py` script: + +``` +$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcids | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2020-03-26-combined-orcids.txt +$ ./resolve-orcids.py -i /tmp/2020-03-26-combined-orcids.txt -o /tmp/2020-03-26-combined-names.txt -d +# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents) +$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml +``` +- I checked the database for likely matches to the author name and then created a CSV with the author names and ORCID iDs: + +``` +dc.contributor.author,cg.creator.id +"King, Brian","Brian King: 0000-0002-7056-9214" +"Ortiz-Crespo, Berta","Berta Ortiz-Crespo: 0000-0002-6664-0815" +"Ekesa, Beatrice","Beatrice Ekesa: 0000-0002-2630-258X" +"Ekesa, B.","Beatrice Ekesa: 0000-0002-2630-258X" +"Ekesa, B.N.","Beatrice Ekesa: 0000-0002-2630-258X" +"Gullotta, G.","Gaia Gullotta: 0000-0002-2240-3869" +``` + +- Running the `add-orcid-identifiers-csv.py` script I added 32 ORCID iDs to items on CGSpace! + +``` +$ ./add-orcid-identifiers-csv.py -i /tmp/2020-03-26-ciat-orcids.csv -db dspace -u dspace -p 'fuuu' +``` + +- Udana from IWMI asked about some items that are missing Altmetric donuts on CGSpace + - One of them had a link to the paper on Nature, but was missing a DOI + - [The second item](https://hdl.handle.net/10568/106899) had no donut so I [tweeted its handle](https://twitter.com/mralanorth/status/1243158045540134913) + - [The third item](https://hdl.handle.net/10568/107258) also had no handle so I [tweeted it](https://twitter.com/mralanorth/status/1243158786392625153) as well +- Abenet pointed out [one item](https://hdl.handle.net/10568/106573) that she had tweeted last week that is missing a donut as well, so I [tweeted it](https://twitter.com/mralanorth/status/1243163710241345536) too + diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index d5667c281..c8315b702 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 bca024e4d..f085681ca 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 787a0f675..8b7de5178 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 f842908ae..e1867ed4e 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 3b474aa6c..7a3f4331e 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 227aab8e7..02d8b3c54 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 90f364492..af9757bf0 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 dbe5eca5e..e2a21dce4 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 80505e3ea..69191de86 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 fd81dcf7a..37c4a964e 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 e9456fad9..2f2c4c30f 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 0bdd6ebab..0b3c6748f 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 5cd6a2bbd..e9104edfd 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 602fb6ffc..f29b5741a 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 2c1c26c87..5dff20398 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 801c64414..2a52674db 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 14afa4a59..a23e4347a 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 6f00120f4..e39da40a4 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 4ab645723..0946612f9 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 5bb95d926..54906f932 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 bc4ca170f..fdba85743 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 d13c7c418..b26b90a9b 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 9cf5a2f20..9abb5741c 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 fda3dc8d9..5886c044f 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 6930e2236..fc614eca1 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 af03fc1d8..9fbac0ed0 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 041232d02..5af9c7c71 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 3ba122650..ca07e689f 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 abba56987..cb1c204b7 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 ae084e2f5..d6b99bbf3 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 ca020fadc..523f57cd2 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 5ddf0cfe4..e3e3c3895 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 b843ad36e..7461342c8 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 889c99771..a5c3a2549 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 4a8201f36..e5f87929c 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 eb3a5000e..f64b016de 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 eed48bb07..23afcc71e 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 8a939796e..8685bf677 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 d8d6a397e..47cbf57cb 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 1df3dd8d9..82aeca233 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 87470c53a..363075bc0 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 3dd9d1818..bd2d5458b 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 dfa1c6e14..20b6b9a25 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 e93f1013f..47491145a 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 0d6cb5883..5cc7aabb8 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 344f5eb85..6bf29fe49 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 68c99515e..157de6c53 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 39fb066f7..2cc4928d0 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 57bc7c7c6..5da077e72 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 97b0bd47e..1b5f08a2f 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 90d3f614c..6081a7484 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 11eb14711..38136caae 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 fbb9535f3..d19932091 100644 --- a/docs/2020-03/index.html +++ b/docs/2020-03/index.html @@ -22,7 +22,7 @@ You need to download this into the DSpace 6.x source and compile it - + @@ -39,7 +39,7 @@ You need to download this into the DSpace 6.x source and compile it "/> - + @@ -49,9 +49,9 @@ You need to download this into the DSpace 6.x source and compile it "@type": "BlogPosting", "headline": "March, 2020", "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-03\/", - "wordCount": "1638", + "wordCount": "1894", "datePublished": "2020-03-02T12:31:30+02:00", - "dateModified": "2020-03-24T15:25:19+02:00", + "dateModified": "2020-03-25T15:58:01+02:00", "author": { "@type": "Person", "name": "Alan Orth" @@ -408,6 +408,40 @@ $ lein run /tmp/affiliations.csv name id
  • I sent Atmire a message to ask if they managed to start working on the DSpace 6 port, as the last communication was twenty-six days ago when they said they were going to secure technical resources to do so
  • Start adapting the dspace role in our Ansible infrastructure playbooks for DSpace 6 support
    • +

    2020-03-26

    + +
    $ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcids | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2020-03-26-combined-orcids.txt
+$ ./resolve-orcids.py -i /tmp/2020-03-26-combined-orcids.txt -o /tmp/2020-03-26-combined-names.txt -d
+# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
+$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
+
    +
    dc.contributor.author,cg.creator.id
+"King, Brian","Brian King: 0000-0002-7056-9214"
+"Ortiz-Crespo, Berta","Berta Ortiz-Crespo: 0000-0002-6664-0815"
+"Ekesa, Beatrice","Beatrice Ekesa: 0000-0002-2630-258X"
+"Ekesa, B.","Beatrice Ekesa: 0000-0002-2630-258X"
+"Ekesa, B.N.","Beatrice Ekesa: 0000-0002-2630-258X"
+"Gullotta, G.","Gaia Gullotta: 0000-0002-2240-3869"
+
    +
    $ ./add-orcid-identifiers-csv.py -i /tmp/2020-03-26-ciat-orcids.csv -db dspace -u dspace -p 'fuuu'
+
    diff --git a/docs/404.html b/docs/404.html index 247a24c96..08c73abe4 100644 --- a/docs/404.html +++ b/docs/404.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/index.html b/docs/categories/index.html index db66c1dfa..211ea38a5 100644 --- a/docs/categories/index.html +++ b/docs/categories/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/index.html b/docs/categories/notes/index.html index 9a02ff71e..8161caa1d 100644 --- a/docs/categories/notes/index.html +++ b/docs/categories/notes/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/page/2/index.html b/docs/categories/notes/page/2/index.html index 1135caa00..c01b4fc8a 100644 --- a/docs/categories/notes/page/2/index.html +++ b/docs/categories/notes/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/page/3/index.html b/docs/categories/notes/page/3/index.html index f02cc3bf7..7e1e88973 100644 --- a/docs/categories/notes/page/3/index.html +++ b/docs/categories/notes/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/page/4/index.html b/docs/categories/notes/page/4/index.html index 59eaca0de..96c8879ac 100644 --- a/docs/categories/notes/page/4/index.html +++ b/docs/categories/notes/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/2/index.html b/docs/categories/page/2/index.html index 6b0ae7f81..35a05cdb8 100644 --- a/docs/categories/page/2/index.html +++ b/docs/categories/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/3/index.html b/docs/categories/page/3/index.html index 801a3d8b6..f85f46216 100644 --- a/docs/categories/page/3/index.html +++ b/docs/categories/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/4/index.html b/docs/categories/page/4/index.html index 84ce8a9e4..eac28edb1 100644 --- a/docs/categories/page/4/index.html +++ b/docs/categories/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/5/index.html b/docs/categories/page/5/index.html index 6cad52b51..a11727995 100644 --- a/docs/categories/page/5/index.html +++ b/docs/categories/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/6/index.html b/docs/categories/page/6/index.html index 15f0c2609..e346e3472 100644 --- a/docs/categories/page/6/index.html +++ b/docs/categories/page/6/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/cgiar-library-migration/index.html b/docs/cgiar-library-migration/index.html index 1ab173f48..625e4dc8e 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 c6cac297c..ce544792a 100644 --- a/docs/cgspace-cgcorev2-migration/index.html +++ b/docs/cgspace-cgcorev2-migration/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/index.html b/docs/index.html index 4a55bd552..bb596d575 100644 --- a/docs/index.html +++ b/docs/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/2/index.html b/docs/page/2/index.html index 386e49cfb..2d6b36032 100644 --- a/docs/page/2/index.html +++ b/docs/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/3/index.html b/docs/page/3/index.html index 2f58c4893..d7d05faf3 100644 --- a/docs/page/3/index.html +++ b/docs/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/4/index.html b/docs/page/4/index.html index 5c124d95e..6a8b1ddca 100644 --- a/docs/page/4/index.html +++ b/docs/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/5/index.html b/docs/page/5/index.html index babc2b230..da8f4c60f 100644 --- a/docs/page/5/index.html +++ b/docs/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/6/index.html b/docs/page/6/index.html index a5472dd10..88bebe615 100644 --- a/docs/page/6/index.html +++ b/docs/page/6/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/index.html b/docs/posts/index.html index 8006f16d2..bee9cc4a0 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/2/index.html b/docs/posts/page/2/index.html index c60f59866..55baf09ad 100644 --- a/docs/posts/page/2/index.html +++ b/docs/posts/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/3/index.html b/docs/posts/page/3/index.html index fb9517c93..7649386de 100644 --- a/docs/posts/page/3/index.html +++ b/docs/posts/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/4/index.html b/docs/posts/page/4/index.html index 399d84ada..8b97a74cf 100644 --- a/docs/posts/page/4/index.html +++ b/docs/posts/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/5/index.html b/docs/posts/page/5/index.html index e330bf90a..1f9c8d6e0 100644 --- a/docs/posts/page/5/index.html +++ b/docs/posts/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/6/index.html b/docs/posts/page/6/index.html index 8b35fbf38..7e9e6c185 100644 --- a/docs/posts/page/6/index.html +++ b/docs/posts/page/6/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 595c8b1eb..2551ea61c 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,27 +4,27 @@ https://alanorth.github.io/cgspace-notes/categories/ - 2020-03-24T15:25:19+02:00 + 2020-03-25T15:58:01+02:00 https://alanorth.github.io/cgspace-notes/ - 2020-03-24T15:25:19+02:00 + 2020-03-25T15:58:01+02:00 https://alanorth.github.io/cgspace-notes/2020-03/ - 2020-03-24T15:25:19+02:00 + 2020-03-25T15:58:01+02:00 https://alanorth.github.io/cgspace-notes/categories/notes/ - 2020-03-24T15:25:19+02:00 + 2020-03-25T15:58:01+02:00 https://alanorth.github.io/cgspace-notes/posts/ - 2020-03-24T15:25:19+02:00 + 2020-03-25T15:58:01+02:00 diff --git a/docs/tags/index.html b/docs/tags/index.html index 63eee22f6..550041c2a 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 64951ac30..3d916b2de 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 cc932528a..aafb526c7 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 b/docs/tags/notes/page/2/index.html index 2947ee943..41ba78e01 100644 --- a/docs/tags/notes/page/2/index.html +++ b/docs/tags/notes/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/notes/page/3/index.html b/docs/tags/notes/page/3/index.html index b3ca9beb9..a9cbb5bc1 100644 --- a/docs/tags/notes/page/3/index.html +++ b/docs/tags/notes/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/2/index.html b/docs/tags/page/2/index.html index 3dc53ea89..d604b6709 100644 --- a/docs/tags/page/2/index.html +++ b/docs/tags/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/3/index.html b/docs/tags/page/3/index.html index 314046146..3d19baac6 100644 --- a/docs/tags/page/3/index.html +++ b/docs/tags/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/4/index.html b/docs/tags/page/4/index.html index 9ef2582b5..25ac60f93 100644 --- a/docs/tags/page/4/index.html +++ b/docs/tags/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/5/index.html b/docs/tags/page/5/index.html index 080bf2179..816ca773a 100644 --- a/docs/tags/page/5/index.html +++ b/docs/tags/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/6/index.html b/docs/tags/page/6/index.html index 4c8fb67cb..f9c8e6cb4 100644 --- a/docs/tags/page/6/index.html +++ b/docs/tags/page/6/index.html @@ -14,7 +14,7 @@ - +