Add notes for 2019-09-19

2024-11-22 06:35:03 +01:00 · 2019-09-19 18:20:04 +03:00 · 2019-09-19 18:20:04 +03:00 · 63a28eff29
commit 63a28eff29
parent 9d5c1a6e13
77 changed files with 262 additions and 83 deletions
--- a/content/posts/2019-09.md
+++ b/content/posts/2019-09.md
@ -152,4 +152,86 @@ dspace.log.2019-09-15:808
 - I restarted Tomcat and the item views came back, but then the Solr statistics cores didn't all load properly
  - After restarting Tomcat once again, both the item views and the Solr statistics cores all came back OK

+## 2019-09-19
+
+- For some reason my podman PostgreSQL container isn't working so I had to use Docker to re-create it for my testing work today:
+
+```
+# docker pull docker.io/library/postgres:9.6-alpine
+# docker create volume dspacedb_data
+# docker run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
+$ createuser -h localhost -U postgres --pwprompt dspacetest
+$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
+$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
+$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost ~/Downloads/cgspace_2019-08-31.backup
+$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
+$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
+```
+
+- Elizabeth from CIAT sent me a list of sixteen authors who need to have their ORCID identifiers tagged with their publications
+  - I manually checked the ORCID profile links to make sure they matched the names
+  - Then I created an input file to use with my `add-orcid-identifiers-csv.py` script:
+
+```
+dc.contributor.author,cg.creator.id
+"Kihara, Job","Job Kihara: 0000-0002-4394-9553"
+"Twyman, Jennifer","Jennifer Twyman: 0000-0002-8581-5668"
+"Ishitani, Manabu","Manabu Ishitani: 0000-0002-6950-4018"
+"Arango, Jacobo","Jacobo Arango: 0000-0002-4828-9398"
+"Chavarriaga Aguirre, Paul","Paul Chavarriaga-Aguirre: 0000-0001-7579-3250"
+"Paul, Birthe","Birthe Paul: 0000-0002-5994-5354"
+"Eitzinger, Anton","Anton Eitzinger: 0000-0001-7317-3381"
+"Hoek, Rein van der","Rein van der Hoek: 0000-0003-4528-7669"
+"Aranzales Rondón, Ericson","Ericson Aranzales Rondon: 0000-0001-7487-9909"
+"Staiger-Rivas, Simone","Simone Staiger: 0000-0002-3539-0817"
+"de Haan, Stef","Stef de Haan: 0000-0001-8690-1886"
+"Pulleman, Mirjam","Mirjam Pulleman: 0000-0001-9950-0176"
+"Abera, Wuletawu","Wuletawu Abera: 0000-0002-3657-5223"
+"Tamene, Lulseged","Lulseged Tamene: 0000-0002-3806-8890"
+"Andrieu, Nadine","Nadine Andrieu: 0000-0001-9558-9302"
+"Ramírez-Villegas, Julián","Julian Ramirez-Villegas: 0000-0002-8044-583X"
+```
+
+- I tested the file on my local development machine with the following invocation:
+
+```
+$ ./add-orcid-identifiers-csv.py -i 2019-09-19-ciat-orcids.csv -db dspace -u dspace -p 'fuuu'
+```
+
+- In my test environment this added 390 ORCID identifier
+- I ran the same updates on CGSpace and DSpace Test and then started a Discovery re-index to force the search index to update
+- Update the PostgreSQL JDBC driver to version 42.2.8 in our [Ansible infrastructure scripts](https://github.com/ilri/rmg-ansible-public)
+  - There is only [one minor fix to a usecase we aren't using](https://github.com/pgjdbc/pgjdbc/issues/1567) so I will deploy this on the servers the next time I do updates
+- Run system updates on DSpace Test (linode19) and reboot it
+- Start looking at IITA's latest round of batch updates that Sisay had [uploaded to DSpace Test](https://dspacetest.cgiar.org/handle/10568/105486) earlier this month
+  - For posterity, IITA's original input file was 20196th.xls and Sisay uploaded it as "IITA_Sep_06" to DSpace Test
+  - Sisay said he did ran the csv-metadata-quality script on the records, but I assume he didn't run the unsafe fixes or AGROVOC checks because I still see unneccessary Unicode, excessive whitespace, one invalid ISBN, missing dates and a few invalid AGROVOC fields
+  - In addition, a few records were missing authorship type
+  - I deleted two invalid AGROVOC terms because they were ambiguous
+  - Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:
+    - `$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id`
+    - I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colum and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)`
+  - I also looked through the IITA subjects to normalize some values
+- Follow up with Marissa again about the CCAFS phase II project tags
+- Generate a list of the top 1500 authors on CGSpace:
+
+```
+dspace=# \copy (SELECT DISTINCT text_value, 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 LIMIT 1500) to /tmp/2019-09-19-top-1500-authors.csv WITH CSV HEADER;
+```
+
+- Then I used `csvcut` to select the column of author names, strip the header and quote characters, and saved the sorted file:
+
+```
+$ csvcut -c text_value /tmp/2019-09-19-top-1500-authors.csv | grep -v text_value | sed 's/"//g' | sort > dspace/config/controlled-vocabularies/dc-contributor-author.xml
+```
+
+- After adding the XML formatting back to the file I formatted it using XML tidy:
+
+```
+$ tidy -xml -utf8 -m -iq -w 0 dspace/config/controlled-vocabularies/dc-contributor-author.xml
+```
+
+- I created and merged [a pull request for the updates](https://github.com/ilri/DSpace/pull/433)
+  - This is the first time we've updated this controlled vocabulary since 2018-09
+
 <!-- vim: set sw=2 ts=2: -->
--- a/docs/2015-11/index.html
+++ b/docs/2015-11/index.html
@ -37,7 +37,7 @@ $ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspac
 78

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--- a/docs/2015-12/index.html
+++ b/docs/2015-12/index.html
@ -37,7 +37,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
 -rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz

 "/>
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--- a/docs/2016-01/index.html
+++ b/docs/2016-01/index.html
@ -27,7 +27,7 @@ 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.
 "/>
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--- a/docs/2016-02/index.html
+++ b/docs/2016-02/index.html
@ -41,7 +41,7 @@ I noticed we have a very interesting list of countries on CGSpace:
 Not only are there 49,000 countries, we have some blanks (25)&hellip;
 Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;
 "/>
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--- a/docs/2016-03/index.html
+++ b/docs/2016-03/index.html
@ -27,7 +27,7 @@ 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&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;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
 "/>
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--- a/docs/2016-04/index.html
+++ b/docs/2016-04/index.html
@ -31,7 +31,7 @@ After running DSpace for over five years I&rsquo;ve never needed to look in any
 This will save us a few gigs of backup space we&rsquo;re paying for on S3
 Also, I noticed the checker log has some errors we should pay attention to:
 "/>
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+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/2016-05/index.html
+++ b/docs/2016-05/index.html
@ -37,7 +37,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
 3168

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--- a/docs/2016-06/index.html
+++ b/docs/2016-06/index.html
@ -33,7 +33,7 @@ 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
 "/>
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--- a/docs/2016-07/index.html
+++ b/docs/2016-07/index.html
@ -47,7 +47,7 @@ text_value

 In this case the select query was showing 95 results before the update
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--- a/docs/2016-08/index.html
+++ b/docs/2016-08/index.html
@ -45,7 +45,7 @@ $ git reset --hard ilri/5_x-prod
 $ git rebase -i dspace-5.5

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--- a/docs/2016-09/index.html
+++ b/docs/2016-09/index.html
@ -37,7 +37,7 @@ It looks like we might be able to use OUs now, instead of DCs:
 $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;

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--- a/docs/2016-10/index.html
+++ b/docs/2016-10/index.html
@ -45,7 +45,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X

 "/>
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--- a/docs/2016-11/index.html
+++ b/docs/2016-11/index.html
@ -27,7 +27,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module


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--- a/docs/2016-12/index.html
+++ b/docs/2016-12/index.html
@ -53,7 +53,7 @@ I&rsquo;ve raised a ticket with Atmire to ask

 Another worrying error from dspace.log is:
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--- a/docs/2017-01/index.html
+++ b/docs/2017-01/index.html
@ -27,7 +27,7 @@ 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&rsquo;t work there either
 I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years
 "/>
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--- a/docs/2017-02/index.html
+++ b/docs/2017-02/index.html
@ -53,7 +53,7 @@ Create issue on GitHub to track the addition of CCAFS Phase II project tags (#30

 Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
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--- a/docs/2017-03/index.html
+++ b/docs/2017-03/index.html
@ -61,7 +61,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
 /Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600&#43;0&#43;0 8-bit CMYK 168KB 0.000u 0:00.000

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--- a/docs/2017-04/index.html
+++ b/docs/2017-04/index.html
@ -47,7 +47,7 @@ Testing the CMYK patch on a collection with 650 items:
 $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt

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--- a/docs/2017-05/index.html
+++ b/docs/2017-05/index.html
@ -15,7 +15,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2017"/>
 <meta name="twitter:description" content="2017-05-01  ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items:  https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683   2017-05-02  Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request  2017-05-04  Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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--- a/docs/2017-06/index.html
+++ b/docs/2017-06/index.html
@ -15,7 +15,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="June, 2017"/>
 <meta name="twitter:description" content="2017-06-01  After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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--- a/docs/2017-07/index.html
+++ b/docs/2017-07/index.html
@ -39,7 +39,7 @@ Merge changes for WLE Phase II theme rename (#329)
 Looking at extracting the metadata registries from ICARDA&rsquo;s MEL DSpace database so we can compare fields with CGSpace
 We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the output into quasi XML:
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--- a/docs/2017-08/index.html
+++ b/docs/2017-08/index.html
@ -59,7 +59,7 @@ 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
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--- a/docs/2017-09/index.html
+++ b/docs/2017-09/index.html
@ -35,7 +35,7 @@ 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&rsquo;s user account is both in the approvers step as well as the group
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--- a/docs/2017-10/index.html
+++ b/docs/2017-10/index.html
@ -37,7 +37,7 @@ There appears to be a pattern but I&rsquo;ll have to look a bit closer and try t

 Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections
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--- a/docs/2017-11/index.html
+++ b/docs/2017-11/index.html
@ -55,7 +55,7 @@ dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue
 COPY 54701

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--- a/docs/2017-12/index.html
+++ b/docs/2017-12/index.html
@ -29,7 +29,7 @@ The logs say &ldquo;Timeout waiting for idle object&rdquo;
 PostgreSQL activity says there are 115 connections currently
 The list of connections to XMLUI and REST API for today:
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--- a/docs/2018-01/index.html
+++ b/docs/2018-01/index.html
@ -163,7 +163,7 @@ 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&rsquo;s Encrypt if it&rsquo;s just a handful of domains
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--- a/docs/2018-02/index.html
+++ b/docs/2018-02/index.html
@ -29,7 +29,7 @@ We don&rsquo;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&rsquo;s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
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--- a/docs/2018-03/index.html
+++ b/docs/2018-03/index.html
@ -23,7 +23,7 @@ Export a CSV of the IITA community metadata for Martin Mueller

 Export a CSV of the IITA community metadata for Martin Mueller
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--- a/docs/2018-04/index.html
+++ b/docs/2018-04/index.html
@ -25,7 +25,7 @@ Catalina logs at least show some memory errors yesterday:
 I tried to test something on DSpace Test but noticed that it&rsquo;s down since god knows when
 Catalina logs at least show some memory errors yesterday:
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--- a/docs/2018-05/index.html
+++ b/docs/2018-05/index.html
@ -37,7 +37,7 @@ 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
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--- a/docs/2018-06/index.html
+++ b/docs/2018-06/index.html
@ -65,7 +65,7 @@ user    8m5.056s
 sys     2m7.289s

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--- a/docs/2018-07/index.html
+++ b/docs/2018-07/index.html
@ -39,7 +39,7 @@ 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.

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--- a/docs/2018-08/index.html
+++ b/docs/2018-08/index.html
@ -57,7 +57,7 @@ The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a la

 I ran all system updates on DSpace Test and rebooted it
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--- a/docs/2018-09/index.html
+++ b/docs/2018-09/index.html
@ -29,7 +29,7 @@ I&rsquo;ll update the DSpace role in our Ansible infrastructure playbooks and ru
 Also, I&rsquo;ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month
 I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:
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--- a/docs/2018-10/index.html
+++ b/docs/2018-10/index.html
@ -25,7 +25,7 @@ I created a GitHub issue to track this #389, because I&rsquo;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&rsquo;m super busy in Nairobi right now
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--- a/docs/2018-11/index.html
+++ b/docs/2018-11/index.html
@ -39,7 +39,7 @@ 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:
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--- a/docs/2018-12/index.html
+++ b/docs/2018-12/index.html
@ -39,7 +39,7 @@ 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
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--- a/docs/2019-01/index.html
+++ b/docs/2019-01/index.html
@ -53,7 +53,7 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
 903 54.70.40.11

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--- a/docs/2019-02/index.html
+++ b/docs/2019-02/index.html
@ -81,7 +81,7 @@ user    0m22.203s
 sys     0m1.979s

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--- a/docs/2019-03/index.html
+++ b/docs/2019-03/index.html
@ -45,7 +45,7 @@ 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
 "/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/2019-04/index.html
+++ b/docs/2019-04/index.html
@ -71,7 +71,7 @@ $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspa
 $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d

 "/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/2019-05/index.html
+++ b/docs/2019-05/index.html
@ -51,7 +51,7 @@ DELETE 1

 But after this I tried to delete the item from the XMLUI and it is still present&hellip;
 "/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/2019-06/index.html
+++ b/docs/2019-06/index.html
@ -37,7 +37,7 @@ Run system updates on CGSpace (linode18) and reboot it

 Skype with Marie-Angélique and Abenet about CG Core v2
 "/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/2019-07/index.html
+++ b/docs/2019-07/index.html
@ -37,7 +37,7 @@ CGSpace

 Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
 "/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/2019-08/index.html
+++ b/docs/2019-08/index.html
@ -49,7 +49,7 @@ After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s luck

 Run system updates on DSpace Test (linode19) and reboot it
 "/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/2019-09/index.html
+++ b/docs/2019-09/index.html
@ -40,7 +40,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-09/" />
 <meta property="article:published_time" content="2019-09-01T10:17:51+03:00" />
-<meta property="article:modified_time" content="2019-09-12T18:21:43+03:00" />
+<meta property="article:modified_time" content="2019-09-15T17:29:48+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="September, 2019"/>
@ -75,7 +75,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
 9124 45.5.186.2

 "/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
@ -85,9 +85,9 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
  "@type": "BlogPosting",
  "headline": "September, 2019",
  "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2019-09\/",
-  "wordCount": "1000",
+  "wordCount": "1636",
  "datePublished": "2019-09-01T10:17:51\x2b03:00",
-  "dateModified": "2019-09-12T18:21:43\x2b03:00",
+  "dateModified": "2019-09-15T17:29:48\x2b03:00",
  "author": {
    "@type": "Person",
    "name": "Alan Orth"
@ -338,6 +338,103 @@ dspace.log.2019-09-15:808
 </ul></li>
 </ul>

+<h2 id="2019-09-19">2019-09-19</h2>
+
+<ul>
+<li><p>For some reason my podman PostgreSQL container isn&rsquo;t working so I had to use Docker to re-create it for my testing work today:</p>
+
+<pre><code># docker pull docker.io/library/postgres:9.6-alpine
+# docker create volume dspacedb_data
+# docker run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
+$ createuser -h localhost -U postgres --pwprompt dspacetest
+$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
+$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
+$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost ~/Downloads/cgspace_2019-08-31.backup
+$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
+$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
+</code></pre></li>
+
+<li><p>Elizabeth from CIAT sent me a list of sixteen authors who need to have their ORCID identifiers tagged with their publications</p>
+
+<ul>
+<li>I manually checked the ORCID profile links to make sure they matched the names</li>
+
+<li><p>Then I created an input file to use with my <code>add-orcid-identifiers-csv.py</code> script:</p>
+
+<pre><code>dc.contributor.author,cg.creator.id
+&quot;Kihara, Job&quot;,&quot;Job Kihara: 0000-0002-4394-9553&quot;
+&quot;Twyman, Jennifer&quot;,&quot;Jennifer Twyman: 0000-0002-8581-5668&quot;
+&quot;Ishitani, Manabu&quot;,&quot;Manabu Ishitani: 0000-0002-6950-4018&quot;
+&quot;Arango, Jacobo&quot;,&quot;Jacobo Arango: 0000-0002-4828-9398&quot;
+&quot;Chavarriaga Aguirre, Paul&quot;,&quot;Paul Chavarriaga-Aguirre: 0000-0001-7579-3250&quot;
+&quot;Paul, Birthe&quot;,&quot;Birthe Paul: 0000-0002-5994-5354&quot;
+&quot;Eitzinger, Anton&quot;,&quot;Anton Eitzinger: 0000-0001-7317-3381&quot;
+&quot;Hoek, Rein van der&quot;,&quot;Rein van der Hoek: 0000-0003-4528-7669&quot;
+&quot;Aranzales Rondón, Ericson&quot;,&quot;Ericson Aranzales Rondon: 0000-0001-7487-9909&quot;
+&quot;Staiger-Rivas, Simone&quot;,&quot;Simone Staiger: 0000-0002-3539-0817&quot;
+&quot;de Haan, Stef&quot;,&quot;Stef de Haan: 0000-0001-8690-1886&quot;
+&quot;Pulleman, Mirjam&quot;,&quot;Mirjam Pulleman: 0000-0001-9950-0176&quot;
+&quot;Abera, Wuletawu&quot;,&quot;Wuletawu Abera: 0000-0002-3657-5223&quot;
+&quot;Tamene, Lulseged&quot;,&quot;Lulseged Tamene: 0000-0002-3806-8890&quot;
+&quot;Andrieu, Nadine&quot;,&quot;Nadine Andrieu: 0000-0001-9558-9302&quot;
+&quot;Ramírez-Villegas, Julián&quot;,&quot;Julian Ramirez-Villegas: 0000-0002-8044-583X&quot;
+</code></pre></li>
+</ul></li>
+
+<li><p>I tested the file on my local development machine with the following invocation:</p>
+
+<pre><code>$ ./add-orcid-identifiers-csv.py -i 2019-09-19-ciat-orcids.csv -db dspace -u dspace -p 'fuuu'
+</code></pre></li>
+
+<li><p>In my test environment this added 390 ORCID identifier</p></li>
+
+<li><p>I ran the same updates on CGSpace and DSpace Test and then started a Discovery re-index to force the search index to update</p></li>
+
+<li><p>Update the PostgreSQL JDBC driver to version 42.2.8 in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a></p>
+
+<ul>
+<li>There is only <a href="https://github.com/pgjdbc/pgjdbc/issues/1567">one minor fix to a usecase we aren&rsquo;t using</a> so I will deploy this on the servers the next time I do updates</li>
+</ul></li>
+
+<li><p>Run system updates on DSpace Test (linode19) and reboot it</p></li>
+
+<li><p>Start looking at IITA&rsquo;s latest round of batch updates that Sisay had <a href="https://dspacetest.cgiar.org/handle/10568/105486">uploaded to DSpace Test</a> earlier this month</p>
+
+<ul>
+<li>For posterity, IITA&rsquo;s original input file was 20196th.xls and Sisay uploaded it as &ldquo;IITA_Sep_06&rdquo; to DSpace Test</li>
+<li>Sisay said he did ran the csv-metadata-quality script on the records, but I assume he didn&rsquo;t run the unsafe fixes or AGROVOC checks because I still see unneccessary Unicode, excessive whitespace, one invalid ISBN, missing dates and a few invalid AGROVOC fields</li>
+<li>In addition, a few records were missing authorship type</li>
+<li>I deleted two invalid AGROVOC terms because they were ambiguous</li>
+<li>Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:</li>
+<li><code>$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id</code></li>
+<li>I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colum and populate it using this GREL: <code>if(cell.recon.matched, cell.recon.match.name, value)</code></li>
+<li>I also looked through the IITA subjects to normalize some values</li>
+</ul></li>
+
+<li><p>Follow up with Marissa again about the CCAFS phase II project tags</p></li>
+
+<li><p>Generate a list of the top 1500 authors on CGSpace:</p>
+
+<pre><code>dspace=# \copy (SELECT DISTINCT text_value, 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 LIMIT 1500) to /tmp/2019-09-19-top-1500-authors.csv WITH CSV HEADER;
+</code></pre></li>
+
+<li><p>Then I used <code>csvcut</code> to select the column of author names, strip the header and quote characters, and saved the sorted file:</p>
+
+<pre><code>$ csvcut -c text_value /tmp/2019-09-19-top-1500-authors.csv | grep -v text_value | sed 's/&quot;//g' | sort &gt; dspace/config/controlled-vocabularies/dc-contributor-author.xml
+</code></pre></li>
+
+<li><p>After adding the XML formatting back to the file I formatted it using XML tidy:</p>
+
+<pre><code>$ tidy -xml -utf8 -m -iq -w 0 dspace/config/controlled-vocabularies/dc-contributor-author.xml
+</code></pre></li>
+
+<li><p>I created and merged <a href="https://github.com/ilri/DSpace/pull/433">a pull request for the updates</a></p>
+
+<ul>
+<li>This is the first time we&rsquo;ve updated this controlled vocabulary since 2018-09</li>
+</ul></li>
+</ul>
+
 <!-- vim: set sw=2 ts=2: -->

  
--- a/docs/404.html
+++ b/docs/404.html
@ -14,7 +14,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="404 Page not found"/>
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+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/categories/index.html
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@ -15,7 +15,7 @@
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+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/categories/notes/index.html
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@ -15,7 +15,7 @@
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--- a/docs/categories/page/2/index.html
+++ b/docs/categories/page/2/index.html
@ -15,7 +15,7 @@
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--- a/docs/categories/page/3/index.html
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@ -15,7 +15,7 @@
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 <meta name="twitter:title" content="Categories"/>
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-<meta name="generator" content="Hugo 0.58.1" />
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--- a/docs/categories/page/4/index.html
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@ -15,7 +15,7 @@
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 <meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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--- a/docs/categories/page/5/index.html
+++ b/docs/categories/page/5/index.html
@ -15,7 +15,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.58.1" />
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--- a/docs/cgiar-library-migration/index.html
+++ b/docs/cgiar-library-migration/index.html
@ -15,7 +15,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="CGIAR Library Migration"/>
 <meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/index.html
+++ b/docs/index.html
@ -15,7 +15,7 @@
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@ -15,7 +15,7 @@
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--- a/docs/page/3/index.html
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@ -15,7 +15,7 @@
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@ -15,7 +15,7 @@
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--- a/docs/page/5/index.html
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@ -15,7 +15,7 @@
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-<meta name="generator" content="Hugo 0.58.1" />
+<meta name="generator" content="Hugo 0.58.2" />


    
--- a/docs/posts/index.html
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@ -15,7 +15,7 @@
 <meta name="twitter:card" content="summary"/>
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@ -15,7 +15,7 @@
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--- a/docs/posts/page/3/index.html
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@ -15,7 +15,7 @@
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--- a/docs/posts/page/4/index.html
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@ -15,7 +15,7 @@
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--- a/docs/posts/page/5/index.html
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@ -15,7 +15,7 @@
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--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@ -4,27 +4,27 @@
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/</loc>
-    <lastmod>2019-09-12T18:21:43+03:00</lastmod>
+    <lastmod>2019-09-15T17:29:48+03:00</lastmod>
  </url>
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
-    <lastmod>2019-09-12T18:21:43+03:00</lastmod>
+    <lastmod>2019-09-15T17:29:48+03:00</lastmod>
  </url>
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
-    <lastmod>2019-09-12T18:21:43+03:00</lastmod>
+    <lastmod>2019-09-15T17:29:48+03:00</lastmod>
  </url>
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/2019-09/</loc>
-    <lastmod>2019-09-12T18:21:43+03:00</lastmod>
+    <lastmod>2019-09-15T17:29:48+03:00</lastmod>
  </url>
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
-    <lastmod>2019-09-12T18:21:43+03:00</lastmod>
+    <lastmod>2019-09-15T17:29:48+03:00</lastmod>
  </url>
  
  <url>
--- a/docs/tags/index.html
+++ b/docs/tags/index.html
@ -15,7 +15,7 @@
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-<meta name="generator" content="Hugo 0.58.1" />
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--- a/docs/tags/notes/index.html
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@ -15,7 +15,7 @@
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