diff --git a/content/posts/2021-02.md b/content/posts/2021-02.md
index 7134bd0af..6889fcaf1 100644
--- a/content/posts/2021-02.md
+++ b/content/posts/2021-02.md
@@ -642,7 +642,7 @@ UPDATE 18659
$ dspace metadata-import -f /tmp/0.csv
```
-- It took FOREVER to import each file... like several hours. MY GOD DSpace 6 is slow.
+- It took FOREVER to import each file... like several hours *each*. MY GOD DSpace 6 is slow.
- Help Dominique Perera debug some issues with the WordPress DSpace importer plugin from Macaroni Bros
- She is not seeing the community list for CGSpace, and I see weird requests like this in the logs:
@@ -653,4 +653,90 @@ $ dspace metadata-import -f /tmp/0.csv
- The first request is OK, but the second one is malformed for sure
+## 2021-02-24
+
+- Export a list of journals for Peter to look through:
+
+```console
+localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.journal", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
+COPY 3345
+```
+
+- Start a fresh harvesting on AReS because Udana mapped some items today and wants to include them in his report:
+
+```console
+$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
+# start indexing in AReS
+```
+
+- Also, I want to include the new series name/number cleanups so it's not a total waste of time
+
+## 2021-02-25
+
+- Hmm the AReS harvest last night seems to have finished successfully, but the number of items is less than I was expecting:
+
+```console
+$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
+{
+ "count" : 99546,
+ "_shards" : {
+ "total" : 1,
+ "successful" : 1,
+ "skipped" : 0,
+ "failed" : 0
+ }
+}
+```
+
+- The current items index has 101380 items... I wonder what happened
+ - I started a new indexing
+
+## 2021-02-26
+
+- Last night's indexing was more successful, there are now 101479 items in the index
+- Yesterday Yousef sent a [pull request](https://github.com/ilri/OpenRXV/pull/77/) for the next/previous buttons on OpenRXV
+ - I tested it this morning and it seems to be working
+
+## 2021-02-28
+
+- Abenet asked me to import seventy-three records for CRP Forests, Trees and Agroforestry
+ - I checked them briefly and found that there were thirty+ journal articles, and none of them had `cg.journal`, `cg.volume`, `cg.issue`, or `dcterms.license` so I spent a little time adding them
+ - I used a GREL expression to extract the journal volume and issue from the citation into new columns:
+
+```console
+value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/\(.*\)/,"")
+value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,"$1")
+```
+
+- This `value.partition` was new to me... and it took me a bit of time to figure out whether I needed to escape the parentheses in the issue number or not (no) and how to reference a capture group with `value.replace`
+- I tried to check the 1095 CIFOR records from last week for duplicates on DSpace Test, but the page says "Processing" and never loads
+ - I don't see any errors in the logs, but there are two jQuery errors in the browser console
+ - I filed [an issue](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=934) with Atmire
+- Upload twelve items to CGSpace for Peter
+- Niroshini from IWMI is still having issues adding WLE subjects to items during the metadata review step in the workflow
+- It seems the BatchEditConsumer log spam is gone since I applied [Atmire's patch](https://github.com/ilri/DSpace/pull/462)
+
+```console
+$ grep -c 'BatchEditConsumer should not have been given' dspace.log.2021-02-[12]*
+dspace.log.2021-02-10:5067
+dspace.log.2021-02-11:2647
+dspace.log.2021-02-12:4231
+dspace.log.2021-02-13:221
+dspace.log.2021-02-14:0
+dspace.log.2021-02-15:0
+dspace.log.2021-02-16:0
+dspace.log.2021-02-17:0
+dspace.log.2021-02-18:0
+dspace.log.2021-02-19:0
+dspace.log.2021-02-20:0
+dspace.log.2021-02-21:0
+dspace.log.2021-02-22:0
+dspace.log.2021-02-23:0
+dspace.log.2021-02-24:0
+dspace.log.2021-02-25:0
+dspace.log.2021-02-26:0
+dspace.log.2021-02-27:0
+dspace.log.2021-02-28:0
+```
+
diff --git a/content/posts/2021-03.md b/content/posts/2021-03.md
new file mode 100644
index 000000000..9d627ca77
--- /dev/null
+++ b/content/posts/2021-03.md
@@ -0,0 +1,97 @@
+---
+title: "March, 2021"
+date: 2021-03-01T10:13:54+02:00
+author: "Alan Orth"
+categories: ["Notes"]
+---
+
+## 2021-03-01
+
+- Discuss some OpenRXV issues with Abdullah from CodeObia
+ - He's trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API
+ - Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies
+
+
+
+## 2021-03-02
+
+- I fixed three build and runtime issues in OpenRXV:
+ - [fix highcharts-angular and ngx-tour-core build](https://github.com/ilri/OpenRXV/pull/80)
+ - [frontend/package.json: Pin @types/ramda at 0.27.34](https://github.com/ilri/OpenRXV/pull/82)
+- Then I merged a few fixes that Abdullah had worked on last week
+
+## 2021-03-03
+
+- I [fixed another frontend build warning on OpenRXV](https://github.com/ilri/OpenRXV/issues/83)
+- Then I [updated the frontend container to use Node.js 12 and Ubuntu 20.04](https://github.com/ilri/OpenRXV/pull/84)
+- Also, I [added a GitHub Actions workflow to build the frontend](https://github.com/ilri/OpenRXV/pull/85)
+- I did some testing of Abdullah's patch for the values mapping search on OpenRXV
+ - It still doesn't work with multi-word values, so I recorded a video with wf-recorder and uploaded it to [the issue](https://github.com/ilri/OpenRXV/issues/43) for him to investigate
+
+## 2021-03-04
+
+- Peter is having issues with the workflow since yesterday
+ - I looked at the Munin stats and see a high number of database locks since yesterday
+
+![PostgreSQL locks week](/cgspace-notes/2021/03/postgres_locks_ALL-week.png)
+![PostgreSQL connections week](/cgspace-notes/2021/03/postgres_connections_cgspace-week.png)
+
+- I looked at the number of connections in PostgreSQL and it's definitely high again:
+
+```console
+$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
+1020
+```
+
+- I reported it to Atmire to take a look, on the [same issue](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=851) we had been tracking this before
+- Abenet asked me to add a new ORCID for ILRI staff member Zoe Campbell
+- I added it to the controlled vocabulary and then tagged her existing items on CGSpace using my `add-orcid-identifier.py` script:
+
+```console
+$ cat 2021-03-04-add-zoe-campbell-orcid.csv
+dc.contributor.author,cg.creator.identifier
+"Campbell, Zoë","Zoe Campbell: 0000-0002-4759-9976"
+"Campbell, Zoe A.","Zoe Campbell: 0000-0002-4759-9976"
+$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p 'fuuu'
+```
+
+- I still need to do cleanup on the journal articles metadata
+ - Peter sent me some cleanups but I can't use them in the search/replace format he gave
+ - I think it's better to export the metadata values with IDs and import cleaned up ones as CSV
+
+```console
+localhost/dspace63= > \COPY (SELECT dspace_object_id AS id, text_value as "cg.journal" FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
+COPY 32087
+```
+
+- I used OpenRefine to remove all journal values that didn't have one of these values: ; ( )
+ - Then I cloned the `cg.journal` field to `cg.volume` and `cg.issue`
+ - I used some GREL expressions like these to extract the journal name, volume, and issue:
+
+```console
+value.partition(';')[0].trim() # to get journal names
+value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,"$1") # to get journal volumes
+value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,"$1") # to get journal issues
+```
+
+- Then I uploaded the changes to CGSpace using `dspace metadata-import`
+- Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
+ - The error was "Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e ..."
+ - I searched the DSpace issue tracker and found several issues reporting this:
+ - [DS-3985 Delete item fails](https://jira.lyrasis.org/browse/DS-3985)
+ - [DS-4004 Authorization denied Exception when trying to delete permanently an item, collection or community as a non-Admin user](https://jira.lyrasis.org/browse/DS-4004)
+ - [DS-4297 Authorization error when trying to delete item by submitter/administrator](https://jira.lyrasis.org/browse/DS-4297)
+ - The issue is apparently with non-admin users who are in the admin and submit groups of the owning collection...
+ - In this case the item was uploaded to the CCAFS Reports collection, and Margarita is a non-admin user who is a member of the collection's admin and submit groups, exactly as the issue described
+ - I added a comment about our issue to [DS-4297](https://jira.lyrasis.org/browse/DS-4297)
+- Yesterday Abenet added me to a WLE collection approver/editer steps so we can try to figure out why Niroshini is having issues adding metadata to Udana's submissions
+ - I edited Udana's submission to CGSpace:
+ - corrected the title
+ - added language English
+ - changed the link to the external item page instead of PDF
+ - added SDGs from the external item page
+ - added AGROVOC subjects from the external item page
+ - added pagination (extent)
+ - changed the license to "other" because CC-BY-NC-ND is not printed anywhere in the PDF or external item page
+
+
diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html
index e31fbefd8..1e6595780 100644
--- a/docs/2015-11/index.html
+++ b/docs/2015-11/index.html
@@ -34,7 +34,7 @@ Last week I had increased the limit from 30 to 60, which seemed to help, but now
$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
78
"/>
-
+
@@ -242,6 +242,8 @@ db.statementpool = true
-
diff --git a/docs/2016-01/index.html b/docs/2016-01/index.html
index 6a4ae576f..0bf37b1dc 100644
--- a/docs/2016-01/index.html
+++ b/docs/2016-01/index.html
@@ -28,7 +28,7 @@ Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_
I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.
Update GitHub wiki for documentation of maintenance tasks.
"/>
-
+
@@ -200,6 +200,8 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {} ; | sor
+
-
diff --git a/docs/2016-02/index.html b/docs/2016-02/index.html
index 94c1fe10b..c73163210 100644
--- a/docs/2016-02/index.html
+++ b/docs/2016-02/index.html
@@ -38,7 +38,7 @@ I noticed we have a very interesting list of countries on CGSpace:
Not only are there 49,000 countries, we have some blanks (25)…
Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”
"/>
-
+
@@ -378,6 +378,8 @@ Bitstream: tést señora alimentación.pdf
+
-
diff --git a/docs/2016-03/index.html b/docs/2016-03/index.html
index f610e2998..5d9a7e984 100644
--- a/docs/2016-03/index.html
+++ b/docs/2016-03/index.html
@@ -28,7 +28,7 @@ Looking at issues with author authorities on CGSpace
For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module
Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server
"/>
-
+
@@ -316,6 +316,8 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
+
-
diff --git a/docs/2016-04/index.html b/docs/2016-04/index.html
index d06ac35c5..3bedec55b 100644
--- a/docs/2016-04/index.html
+++ b/docs/2016-04/index.html
@@ -32,7 +32,7 @@ After running DSpace for over five years I’ve never needed to look in any
This will save us a few gigs of backup space we’re paying for on S3
Also, I noticed the checker log has some errors we should pay attention to:
"/>
-
+
@@ -495,6 +495,8 @@ dspace.log.2016-04-27:7271
+
-
diff --git a/docs/2016-06/index.html b/docs/2016-06/index.html
index 3809c78ed..e85159c3a 100644
--- a/docs/2016-06/index.html
+++ b/docs/2016-06/index.html
@@ -34,7 +34,7 @@ This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRec
You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
"/>
-
+
@@ -409,6 +409,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
+
-
diff --git a/docs/2016-07/index.html b/docs/2016-07/index.html
index 4a58b6159..40e9f6358 100644
--- a/docs/2016-07/index.html
+++ b/docs/2016-07/index.html
@@ -44,7 +44,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
In this case the select query was showing 95 results before the update
"/>
-
+
@@ -325,6 +325,8 @@ discovery.index.authority.ignore-variants=true
+
-
diff --git a/docs/2016-12/index.html b/docs/2016-12/index.html
index 2603b7d5c..5ebd3ed39 100644
--- a/docs/2016-12/index.html
+++ b/docs/2016-12/index.html
@@ -46,7 +46,7 @@ I see thousands of them in the logs for the last few months, so it’s not r
I’ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:
"/>
-
+
@@ -784,6 +784,8 @@ $ exit
+
-
diff --git a/docs/2017-01/index.html b/docs/2017-01/index.html
index df67f408d..89031d36e 100644
--- a/docs/2017-01/index.html
+++ b/docs/2017-01/index.html
@@ -28,7 +28,7 @@ I checked to see if the Solr sharding task that is supposed to run on January 1s
I tested on DSpace Test as well and it doesn’t work there either
I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years
"/>
-
+
@@ -369,6 +369,8 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
+
-
diff --git a/docs/2017-02/index.html b/docs/2017-02/index.html
index 41fb20bb4..ea98e1aa7 100644
--- a/docs/2017-02/index.html
+++ b/docs/2017-02/index.html
@@ -50,7 +50,7 @@ DELETE 1
Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)
Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name
"/>
-
+
@@ -424,6 +424,8 @@ COPY 1968
+
-
diff --git a/docs/2017-07/index.html b/docs/2017-07/index.html
index 37efc4762..3475fce06 100644
--- a/docs/2017-07/index.html
+++ b/docs/2017-07/index.html
@@ -36,7 +36,7 @@ Merge changes for WLE Phase II theme rename (#329)
Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
"/>
-
+
@@ -275,6 +275,8 @@ delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and
+
-
diff --git a/docs/2017-08/index.html b/docs/2017-08/index.html
index 0b3ec3400..1005fd614 100644
--- a/docs/2017-08/index.html
+++ b/docs/2017-08/index.html
@@ -60,7 +60,7 @@ This was due to newline characters in the dc.description.abstract column, which
I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
"/>
-
+
@@ -517,6 +517,8 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
+
-
diff --git a/docs/2017-09/index.html b/docs/2017-09/index.html
index 7360bc25c..62c3c5cc2 100644
--- a/docs/2017-09/index.html
+++ b/docs/2017-09/index.html
@@ -32,7 +32,7 @@ Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two
Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group
"/>
-
+
@@ -659,6 +659,8 @@ Cert Status: good
+
-
diff --git a/docs/2017-10/index.html b/docs/2017-10/index.html
index 39a889c72..1d8f1e3d6 100644
--- a/docs/2017-10/index.html
+++ b/docs/2017-10/index.html
@@ -34,7 +34,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine
Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections
"/>
-
+
@@ -443,6 +443,8 @@ session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
+
-
diff --git a/docs/2017-11/index.html b/docs/2017-11/index.html
index ef0eac9c9..7112cda21 100644
--- a/docs/2017-11/index.html
+++ b/docs/2017-11/index.html
@@ -48,7 +48,7 @@ Generate list of authors on CGSpace for Peter to go through and correct:
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
"/>
-
+
@@ -944,6 +944,8 @@ $ cat dspace.log.2017-11-28 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | u
+
-
diff --git a/docs/2017-12/index.html b/docs/2017-12/index.html
index 54e7986be..e7121eda3 100644
--- a/docs/2017-12/index.html
+++ b/docs/2017-12/index.html
@@ -30,7 +30,7 @@ The logs say “Timeout waiting for idle object”
PostgreSQL activity says there are 115 connections currently
The list of connections to XMLUI and REST API for today:
"/>
-
+
@@ -783,6 +783,8 @@ DELETE 20
+
-
diff --git a/docs/2018-01/index.html b/docs/2018-01/index.html
index 11e52e9fa..7f3d3361f 100644
--- a/docs/2018-01/index.html
+++ b/docs/2018-01/index.html
@@ -150,7 +150,7 @@ dspace.log.2018-01-02:34
Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains
"/>
-
+
@@ -1452,6 +1452,8 @@ Catalina:type=Manager,context=/,host=localhost activeSessions 8
+
-
diff --git a/docs/2018-02/index.html b/docs/2018-02/index.html
index 6fe722fea..6b4e9ef1e 100644
--- a/docs/2018-02/index.html
+++ b/docs/2018-02/index.html
@@ -30,7 +30,7 @@ We don’t need to distinguish between internal and external works, so that
Yesterday I figured out how to monitor DSpace sessions using JMX
I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
"/>
-
+
@@ -1039,6 +1039,8 @@ UPDATE 3
+
-
diff --git a/docs/2018-03/index.html b/docs/2018-03/index.html
index b0b518434..082bc4e1b 100644
--- a/docs/2018-03/index.html
+++ b/docs/2018-03/index.html
@@ -24,7 +24,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
Export a CSV of the IITA community metadata for Martin Mueller
"/>
-
+
@@ -585,6 +585,8 @@ Fixed 5 occurences of: GENEBANKS
+
-
diff --git a/docs/2018-04/index.html b/docs/2018-04/index.html
index 22b3c0bce..aa56a9436 100644
--- a/docs/2018-04/index.html
+++ b/docs/2018-04/index.html
@@ -26,7 +26,7 @@ Catalina logs at least show some memory errors yesterday:
I tried to test something on DSpace Test but noticed that it’s down since god knows when
Catalina logs at least show some memory errors yesterday:
"/>
-
+
@@ -594,6 +594,8 @@ $ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-
+
-
diff --git a/docs/2018-05/index.html b/docs/2018-05/index.html
index 7d54d6291..48b7173b0 100644
--- a/docs/2018-05/index.html
+++ b/docs/2018-05/index.html
@@ -38,7 +38,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
Then I reduced the JVM heap size from 6144 back to 5120m
Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use
"/>
-
+
@@ -523,6 +523,8 @@ $ psql -h localhost -U postgres dspacetest
+
-
diff --git a/docs/2018-07/index.html b/docs/2018-07/index.html
index a20da2d21..db778383c 100644
--- a/docs/2018-07/index.html
+++ b/docs/2018-07/index.html
@@ -36,7 +36,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r
There is insufficient memory for the Java Runtime Environment to continue.
"/>
-
+
@@ -569,6 +569,8 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
+
-
diff --git a/docs/2018-08/index.html b/docs/2018-08/index.html
index e8555afb1..42a35b7e9 100644
--- a/docs/2018-08/index.html
+++ b/docs/2018-08/index.html
@@ -46,7 +46,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did
The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes
I ran all system updates on DSpace Test and rebooted it
"/>
-
+
@@ -442,6 +442,8 @@ $ dspace database migrate ignored
+
-
diff --git a/docs/2018-09/index.html b/docs/2018-09/index.html
index b704a4160..88b0a5e14 100644
--- a/docs/2018-09/index.html
+++ b/docs/2018-09/index.html
@@ -30,7 +30,7 @@ I’ll update the DSpace role in our Ansible infrastructure playbooks and ru
Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month
I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:
"/>
-
+
@@ -748,6 +748,8 @@ UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_f
+
-
diff --git a/docs/2018-10/index.html b/docs/2018-10/index.html
index 6c8ebd401..9c841ed9d 100644
--- a/docs/2018-10/index.html
+++ b/docs/2018-10/index.html
@@ -26,7 +26,7 @@ I created a GitHub issue to track this #389, because I’m super busy in Nai
Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items
I created a GitHub issue to track this #389, because I’m super busy in Nairobi right now
"/>
-
+
@@ -656,6 +656,8 @@ $ curl -X GET -H "Content-Type: application/json" -H "Accept: app
+
-
diff --git a/docs/2018-11/index.html b/docs/2018-11/index.html
index 657f0f30d..c3857ec47 100644
--- a/docs/2018-11/index.html
+++ b/docs/2018-11/index.html
@@ -36,7 +36,7 @@ Send a note about my dspace-statistics-api to the dspace-tech mailing list
Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage
Today these are the top 10 IPs:
"/>
-
+
@@ -553,6 +553,8 @@ $ dspace dsrun org.dspace.eperson.Groomer -a -b 11/27/2016 -d
+
-
diff --git a/docs/2018-12/index.html b/docs/2018-12/index.html
index b5797dbe9..3a8b796b5 100644
--- a/docs/2018-12/index.html
+++ b/docs/2018-12/index.html
@@ -36,7 +36,7 @@ Then I ran all system updates and restarted the server
I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week
"/>
-
+
@@ -594,6 +594,8 @@ UPDATE 1
+
-
diff --git a/docs/2019-01/index.html b/docs/2019-01/index.html
index 62f230730..257d93fd6 100644
--- a/docs/2019-01/index.html
+++ b/docs/2019-01/index.html
@@ -50,7 +50,7 @@ I don’t see anything interesting in the web server logs around that time t
357 207.46.13.1
903 54.70.40.11
"/>
-
+
@@ -1264,6 +1264,8 @@ identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/
+
-
diff --git a/docs/2019-03/index.html b/docs/2019-03/index.html
index 818eb1185..396f977eb 100644
--- a/docs/2019-03/index.html
+++ b/docs/2019-03/index.html
@@ -46,7 +46,7 @@ Most worryingly, there are encoding errors in the abstracts for eleven items, fo
I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs
"/>
-
+
@@ -1208,6 +1208,8 @@ sys 0m2.551s
+
-
diff --git a/docs/2019-05/index.html b/docs/2019-05/index.html
index 9a4b4f3a9..6f31a29ef 100644
--- a/docs/2019-05/index.html
+++ b/docs/2019-05/index.html
@@ -48,7 +48,7 @@ DELETE 1
But after this I tried to delete the item from the XMLUI and it is still present…
"/>
-
+
@@ -631,6 +631,8 @@ COPY 64871
+
-
diff --git a/docs/2019-06/index.html b/docs/2019-06/index.html
index 289584647..c9654cf6e 100644
--- a/docs/2019-06/index.html
+++ b/docs/2019-06/index.html
@@ -34,7 +34,7 @@ Run system updates on CGSpace (linode18) and reboot it
Skype with Marie-Angélique and Abenet about CG Core v2
"/>
-
+
@@ -317,6 +317,8 @@ UPDATE 2
+
-
diff --git a/docs/2019-07/index.html b/docs/2019-07/index.html
index d2eeb95e8..f10d82794 100644
--- a/docs/2019-07/index.html
+++ b/docs/2019-07/index.html
@@ -38,7 +38,7 @@ CGSpace
Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
"/>
-
+
@@ -554,6 +554,8 @@ issn.validate('1020-3362')
+
-
diff --git a/docs/2019-08/index.html b/docs/2019-08/index.html
index 140ee9c35..d7dbc4810 100644
--- a/docs/2019-08/index.html
+++ b/docs/2019-08/index.html
@@ -46,7 +46,7 @@ After rebooting, all statistics cores were loaded… wow, that’s luck
Run system updates on DSpace Test (linode19) and reboot it
"/>
-
+
@@ -573,6 +573,8 @@ sys 2m27.496s
+
-
diff --git a/docs/2019-09/index.html b/docs/2019-09/index.html
index 0cb6105a2..c86d58fd4 100644
--- a/docs/2019-09/index.html
+++ b/docs/2019-09/index.html
@@ -72,7 +72,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
"/>
-
+
@@ -581,6 +581,8 @@ $ csv-metadata-quality -i /tmp/clarisa-institutions.csv -o /tmp/clarisa-institut
+
-
diff --git a/docs/2019-12/index.html b/docs/2019-12/index.html
index be6780957..33a4f0c0e 100644
--- a/docs/2019-12/index.html
+++ b/docs/2019-12/index.html
@@ -46,7 +46,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# dpkg -C
# reboot
"/>
-
+
@@ -404,6 +404,8 @@ UPDATE 1
+
-
diff --git a/docs/2020-04/index.html b/docs/2020-04/index.html
index 096a39a90..6fb0bf9ad 100644
--- a/docs/2020-04/index.html
+++ b/docs/2020-04/index.html
@@ -48,7 +48,7 @@ The third item now has a donut with score 1 since I tweeted it last week
On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week
"/>
-
+
@@ -658,6 +658,8 @@ $ psql -c 'select * from pg_stat_activity' | wc -l
+
-
diff --git a/docs/2020-05/index.html b/docs/2020-05/index.html
index 15c8874c9..d6855c0c5 100644
--- a/docs/2020-05/index.html
+++ b/docs/2020-05/index.html
@@ -34,7 +34,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
"/>
-
+
@@ -477,6 +477,8 @@ Caused by: java.lang.NullPointerException
+
-
diff --git a/docs/2020-06/index.html b/docs/2020-06/index.html
index e7715e642..6e1bd6088 100644
--- a/docs/2020-06/index.html
+++ b/docs/2020-06/index.html
@@ -36,7 +36,7 @@ I sent Atmire the dspace.log from today and told them to log into the server to
In other news, I checked the statistics API on DSpace 6 and it’s working
I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:
"/>
-
+
@@ -811,6 +811,8 @@ $ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp
+
-
diff --git a/docs/2020-07/index.html b/docs/2020-07/index.html
index 6c93dbdff..e280f1f24 100644
--- a/docs/2020-07/index.html
+++ b/docs/2020-07/index.html
@@ -38,7 +38,7 @@ I restarted Tomcat and PostgreSQL and the issue was gone
Since I was restarting Tomcat anyways I decided to redeploy the latest changes from the 5_x-prod branch and I added a note about COVID-19 items to the CGSpace frontpage at Peter’s request
"/>
-
+
@@ -1142,6 +1142,8 @@ Fixed 4 occurences of: Muloi, D.M.
+
-
diff --git a/docs/2020-08/index.html b/docs/2020-08/index.html
index f1bc63307..09ed362af 100644
--- a/docs/2020-08/index.html
+++ b/docs/2020-08/index.html
@@ -36,7 +36,7 @@ It is class based so I can easily add support for other vocabularies, and the te
"/>
-
+
@@ -798,6 +798,8 @@ $ grep -c added /tmp/2020-08-27-countrycodetagger.log
+
-
diff --git a/docs/2020-09/index.html b/docs/2020-09/index.html
index a5b06cc51..c84d8a2ce 100644
--- a/docs/2020-09/index.html
+++ b/docs/2020-09/index.html
@@ -48,7 +48,7 @@ I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
"/>
-
+
@@ -717,6 +717,8 @@ solr_query_params = {
+
-
diff --git a/docs/2020-11/index.html b/docs/2020-11/index.html
index b32889171..cab5d45dd 100644
--- a/docs/2020-11/index.html
+++ b/docs/2020-11/index.html
@@ -32,7 +32,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat
"/>
-
+
@@ -731,6 +731,8 @@ $ ./fix-metadata-values.py -i 2020-11-30-fix-hung-orcid.csv -db dspace63 -u dspa
+
-
diff --git a/docs/2021-01/index.html b/docs/2021-01/index.html
index dd4c50175..8b0f61c26 100644
--- a/docs/2021-01/index.html
+++ b/docs/2021-01/index.html
@@ -50,7 +50,7 @@ For example, this item has 51 views on CGSpace, but 0 on AReS
"/>
-
+
@@ -688,6 +688,8 @@ java.lang.IllegalArgumentException: Invalid character found in the request targe
+
It took FOREVER to import each file… like several hours. MY GOD DSpace 6 is slow.
+
It took FOREVER to import each file… like several hours each. MY GOD DSpace 6 is slow.
Help Dominique Perera debug some issues with the WordPress DSpace importer plugin from Macaroni Bros
She is not seeing the community list for CGSpace, and I see weird requests like this in the logs:
@@ -791,7 +791,94 @@ UPDATE 18659
The first request is OK, but the second one is malformed for sure
-
+
2021-02-24
+
+
Export a list of journals for Peter to look through:
+
+
localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.journal", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
+COPY 3345
+
+
Start a fresh harvesting on AReS because Udana mapped some items today and wants to include them in his report:
+
+
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
+# start indexing in AReS
+
+
Also, I want to include the new series name/number cleanups so it’s not a total waste of time
+
+
2021-02-25
+
+
Hmm the AReS harvest last night seems to have finished successfully, but the number of items is less than I was expecting:
The current items index has 101380 items… I wonder what happened
+
+
I started a new indexing
+
+
+
+
2021-02-26
+
+
Last night’s indexing was more successful, there are now 101479 items in the index
+
Yesterday Yousef sent a pull request for the next/previous buttons on OpenRXV
+
+
I tested it this morning and it seems to be working
+
+
+
+
2021-02-28
+
+
Abenet asked me to import seventy-three records for CRP Forests, Trees and Agroforestry
+
+
I checked them briefly and found that there were thirty+ journal articles, and none of them had cg.journal, cg.volume, cg.issue, or dcterms.license so I spent a little time adding them
+
I used a GREL expression to extract the journal volume and issue from the citation into new columns:
This value.partition was new to me… and it took me a bit of time to figure out whether I needed to escape the parentheses in the issue number or not (no) and how to reference a capture group with value.replace
+
I tried to check the 1095 CIFOR records from last week for duplicates on DSpace Test, but the page says “Processing” and never loads
+
+
I don’t see any errors in the logs, but there are two jQuery errors in the browser console
I still need to do cleanup on the journal articles metadata
+
+
Peter sent me some cleanups but I can’t use them in the search/replace format he gave
+
I think it’s better to export the metadata values with IDs and import cleaned up ones as CSV
+
+
+
+
localhost/dspace63= > \COPY (SELECT dspace_object_id AS id, text_value as "cg.journal" FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
+COPY 32087
+
+
I used OpenRefine to remove all journal values that didn’t have one of these values: ; ( )
+
+
Then I cloned the cg.journal field to cg.volume and cg.issue
+
I used some GREL expressions like these to extract the journal name, volume, and issue:
+
+
+
+
value.partition(';')[0].trim() # to get journal names
+value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,"$1") # to get journal volumes
+value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,"$1") # to get journal issues
+
+
Then I uploaded the changes to CGSpace using dspace metadata-import
+
Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
+
+
The error was “Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e …”
+
I searched the DSpace issue tracker and found several issues reporting this:
+
The issue is apparently with non-admin users who are in the admin and submit groups of the owning collection…
+
In this case the item was uploaded to the CCAFS Reports collection, and Margarita is a non-admin user who is a member of the collection’s admin and submit groups, exactly as the issue described
Yesterday Abenet added me to a WLE collection approver/editer steps so we can try to figure out why Niroshini is having issues adding metadata to Udana’s submissions
+
+
I edited Udana’s submission to CGSpace:
+
+
corrected the title
+
added language English
+
changed the link to the external item page instead of PDF
+
added SDGs from the external item page
+
added AGROVOC subjects from the external item page
+
added pagination (extent)
+
changed the license to “other” because CC-BY-NC-ND is not printed anywhere in the PDF or external item page
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/2021/03/postgres_connections_cgspace-week.png b/docs/2021/03/postgres_connections_cgspace-week.png
new file mode 100644
index 000000000..0a911b038
Binary files /dev/null and b/docs/2021/03/postgres_connections_cgspace-week.png differ
diff --git a/docs/2021/03/postgres_locks_ALL-week.png b/docs/2021/03/postgres_locks_ALL-week.png
new file mode 100644
index 000000000..59eafded7
Binary files /dev/null and b/docs/2021/03/postgres_locks_ALL-week.png differ
diff --git a/docs/404.html b/docs/404.html
index 4ef7f1626..3261ba8d1 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -17,7 +17,7 @@
-
+
@@ -95,6 +95,8 @@
+
I tried to run the AtomicStatisticsUpdateCLI CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
-
-
I sent Atmire the dspace.log from today and told them to log into the server to debug the process
-
-
-
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: