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133
content/posts/2021-03.md
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@ -367,4 +367,137 @@ $ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
- I also made some minor optimizations in the Pandas code
- I [tagged version 0.4.7 of csv-metadata-quality on GitHub](https://github.com/ilri/csv-metadata-quality/releases/tag/v0.4.7)
## 2021-03-18
- I added the ability to check for, and fix, "mojibake" characters in csv-metadata-quality
## 2021-03-21
- Last week Atmire asked me which browser I was using to test the duplicate checker, which I had [reported](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=934) as not loading
- I tried to load it in Chrome and it works... hmmm
- Back up the current `openrxv-items-final` index to start a fresh AReS Harvest:
```console
$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-2021-03-21
$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
```
- Then start harvesting in the AReS Explorer admin UI
## 2021-03-22
- The harvesting on AReS yesterday completed, but somehow I have twice the number of items:
```console
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
{
"count" : 206204,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
```
- Hmmm and even my backup index has a strange number of items:
```console
$ curl -s 'http://localhost:9200/openrxv-items-final-2021-03-21/_count?q=*&pretty'
{
"count" : 844,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
```
- I deleted all indexes and re-created the openrxv-items alias:
```console
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
...
"openrxv-items-temp": {
"aliases": {}
},
"openrxv-items-final": {
"aliases": {
"openrxv-items": {}
}
}
```
- Then I started a new harvesting
- I switched the Node.js in the [Ansible infrastructure scripts](https://github.com/ilri/rmg-ansible-public) to v12 since v10 will cease to be supported soon
- I re-deployed DSpace Test (linode26) with Node.js 12 and restarted the server
- The AReS harvest finally finished, with 1047 pages of items, but the `openrxv-items-final` index is empty and the `openrxv-items-temp` index has a 103,000 items:
```console
$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
{
"count" : 103162,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
```
- I tried to clone the temp index to the final, but got an error:
```console
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
{"error":{"root_cause":[{"type":"resource_already_exists_exception","reason":"index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists","index_uuid":"LmxH-rQsTRmTyWex2d8jxw","index":"openrxv-items-final"}],"type":"resource_already_exists_exception","reason":"index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists","index_uuid":"LmxH-rQsTRmTyWex2d8jxw","index":"openrxv-items-final"},"status":400}%
```
- I looked in the Docker logs for Elasticsearch and saw a few memory errors:
```console
java.lang.OutOfMemoryError: Java heap space
```
- According to `/usr/share/elasticsearch/config/jvm.options` in the Elasticsearch container the default JVM heap is 1g
- I see the running Java process has `-Xms 1g -Xmx 1g` in its process invocation so I guess that it must be indeed using 1g
- We can [change the heap size with the ES_JAVA_OPTS environment variable](https://www.elastic.co/guide/en/elasticsearch/reference/current/docker.html)
- Or perhaps better, we should [use a jvm.options.d file](https://www.elastic.co/guide/en/elasticsearch/reference/master/jvm-options.html) because if you use the environment variable it overrides all other JVM options from the default `jvm.options`
- I tried to set memory to 1536m by binding an options file and restarting the container, but it didn't seem to work
- Nevertheless, after restarting I see 103,000 items in the Explorer...
- But the indexes are still kinda messed up... the `openrxv-items` index is an alias of the wrong index!
```console
"openrxv-items-final": {
"aliases": {}
},
"openrxv-items-temp": {
"aliases": {
"openrxv-items": {}
}
},
```
## 2021-03-23
- For reference you can also get the Elasticsearch JVM stats from the API:
```console
$ curl -s 'http://localhost:9200/_nodes/jvm?human' | python -m json.tool
```
- I re-deployed AReS with 1.5GB of heap using the `ES_JAVA_OPTS` environment variable
- It turns out that this *is* the recommended way to set the heap: https://www.elastic.co/guide/en/elasticsearch/reference/7.6/jvm-options.html
- Then I fixed the aliases to make sure `openrxv-items` was an alias of `openrxv-items-final`, similar to how I did a few weeks ago
- I re-created the temp index:
```console
$ curl -XPUT 'http://localhost:9200/openrxv-items-temp'
```
<!-- vim: set sw=2 ts=2: -->

2
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@ -34,7 +34,7 @@ Last week I had increased the limit from 30 to 60, which seemed to help, but now
$ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspace
78
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@ -36,7 +36,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
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@ -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.
"/>
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@ -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)&hellip;
Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;
"/>
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2
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@ -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&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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2
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@ -32,7 +32,7 @@ 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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2
docs/2016-05/index.html
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@ -34,7 +34,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
# awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168
"/>
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2
docs/2016-06/index.html
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@ -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
"/>
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2
docs/2016-07/index.html
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@ -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
"/>
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2
docs/2016-08/index.html
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@ -42,7 +42,7 @@ $ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
"/>
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2
docs/2016-09/index.html
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@ -34,7 +34,7 @@ It looks like we might be able to use OUs now, instead of DCs:
$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
"/>
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2
docs/2016-10/index.html
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@ -42,7 +42,7 @@ 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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2
docs/2016-11/index.html
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@ -26,7 +26,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286)
"/>
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docs/2016-12/index.html
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@ -46,7 +46,7 @@ I see thousands of them in the logs for the last few months, so it&rsquo;s not r
I&rsquo;ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:
"/>
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2
docs/2017-01/index.html
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@ -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&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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2
docs/2017-02/index.html
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@ -50,7 +50,7 @@ DELETE 1
Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)
Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
"/>
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2
docs/2017-03/index.html
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@ -54,7 +54,7 @@ Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing reg
$ 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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2
docs/2017-04/index.html
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@ -40,7 +40,7 @@ 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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2
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@ -18,7 +18,7 @@
<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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@ -18,7 +18,7 @@
<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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2
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@ -36,7 +36,7 @@ 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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2
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@ -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
"/>
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2
docs/2017-09/index.html
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@ -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&rsquo;s user account is both in the approvers step as well as the group
"/>
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2
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@ -34,7 +34,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
There appears to be a pattern but I&rsquo;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
"/>
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2
docs/2017-11/index.html
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@ -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 = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
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@ -30,7 +30,7 @@ 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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@ -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&rsquo;s Encrypt if it&rsquo;s just a handful of domains
"/>
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@ -30,7 +30,7 @@ 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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@ -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
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@ -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&rsquo;s down since god knows when
Catalina logs at least show some memory errors yesterday:
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@ -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
"/>
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@ -58,7 +58,7 @@ real 74m42.646s
user 8m5.056s
sys 2m7.289s
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@ -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.
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@ -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&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes
I ran all system updates on DSpace Test and rebooted it
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@ -30,7 +30,7 @@ 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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@ -26,7 +26,7 @@ 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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docs/2018-11/index.html
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@ -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:
"/>
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@ -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
"/>
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@ -50,7 +50,7 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
357 207.46.13.1
903 54.70.40.11
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@ -72,7 +72,7 @@ real 0m19.873s
user 0m22.203s
sys 0m1.979s
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@ -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
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@ -64,7 +64,7 @@ $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u ds
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -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 &#39;fuuu&#39; -m 231 -f cg.coverage.region -d
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@ -48,7 +48,7 @@ DELETE 1
But after this I tried to delete the item from the XMLUI and it is still present&hellip;
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@ -34,7 +34,7 @@ Run system updates on CGSpace (linode18) and reboot it
Skype with Marie-Angélique and Abenet about CG Core v2
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@ -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
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@ -46,7 +46,7 @@ After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s luck
Run system updates on DSpace Test (linode19) and reboot it
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@ -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
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@ -18,7 +18,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="October, 2019"/>
<meta name="twitter:description" content="2019-10-01 Udana from IWMI asked me for a CSV export of their community on CGSpace I exported it, but a quick run through the csv-metadata-quality tool shows that there are some low-hanging fruits we can fix before I send him the data I will limit the scope to the titles, regions, subregions, and river basins for now to manually fix some non-breaking spaces (U&#43;00A0) there that would otherwise be removed by the csv-metadata-quality script&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c &#39;id,dc."/>
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@ -58,7 +58,7 @@ Let&rsquo;s see how many of the REST API requests were for bitstreams (because t
# zcat --force /var/log/nginx/rest.log.*.gz | grep -E &quot;[0-9]{1,2}/Oct/2019&quot; | grep -c -E &quot;/rest/bitstreams&quot;
106781
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@ -46,7 +46,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# dpkg -C
# reboot
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@ -56,7 +56,7 @@ I tweeted the CGSpace repository link
"/>
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@ -38,7 +38,7 @@ The code finally builds and runs with a fresh install
"/>
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@ -42,7 +42,7 @@ You need to download this into the DSpace 6.x source and compile it
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@ -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
"/>
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@ -34,7 +34,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
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2
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@ -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&rsquo;s working
I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:
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2
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@ -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&rsquo;s request
"/>
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2
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@ -36,7 +36,7 @@ It is class based so I can easily add support for other vocabularies, and the te
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2
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@ -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
"/>
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@ -44,7 +44,7 @@ During the FlywayDB migration I got an error:
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2
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@ -32,7 +32,7 @@ So far we&rsquo;ve spent at least fifty hours to process the statistics and stat
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2
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@ -36,7 +36,7 @@ I started processing those (about 411,000 records):
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2
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@ -50,7 +50,7 @@ For example, this item has 51 views on CGSpace, but 0 on AReS
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2
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@ -60,7 +60,7 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
}
}
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@ -19,7 +19,7 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-03/" />
<meta property="article:published_time" content="2021-03-01T10:13:54+02:00" />
<meta property="article:modified_time" content="2021-03-14T21:34:07+02:00" />
<meta property="article:modified_time" content="2021-03-17T14:57:45+02:00" />
@ -34,7 +34,7 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst
"/>
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@ -44,9 +44,9 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst
"@type": "BlogPosting",
"headline": "March, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-03/",
"wordCount": "2337",
"wordCount": "2914",
"datePublished": "2021-03-01T10:13:54+02:00",
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"dateModified": "2021-03-17T14:57:45+02:00",
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"@type": "Person",
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@ -522,7 +522,130 @@ $ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Conte
<li>I also made some minor optimizations in the Pandas code</li>
<li>I <a href="https://github.com/ilri/csv-metadata-quality/releases/tag/v0.4.7">tagged version 0.4.7 of csv-metadata-quality on GitHub</a></li>
</ul>
<!-- raw HTML omitted -->
<h2 id="2021-03-18">2021-03-18</h2>
<ul>
<li>I added the ability to check for, and fix, &ldquo;mojibake&rdquo; characters in csv-metadata-quality</li>
</ul>
<h2 id="2021-03-21">2021-03-21</h2>
<ul>
<li>Last week Atmire asked me which browser I was using to test the duplicate checker, which I had <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=934">reported</a> as not loading
<ul>
<li>I tried to load it in Chrome and it works&hellip; hmmm</li>
</ul>
</li>
<li>Back up the current <code>openrxv-items-final</code> index to start a fresh AReS Harvest:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-2021-03-21
$ curl -X PUT &quot;localhost:9200/openrxv-items-final/_settings&quot; -H 'Content-Type: application/json' -d'{&quot;settings&quot;: {&quot;index.blocks.write&quot;: false}}'
</code></pre><ul>
<li>Then start harvesting in the AReS Explorer admin UI</li>
</ul>
<h2 id="2021-03-22">2021-03-22</h2>
<ul>
<li>The harvesting on AReS yesterday completed, but somehow I have twice the number of items:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&amp;pretty'
{
&quot;count&quot; : 206204,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
</code></pre><ul>
<li>Hmmm and even my backup index has a strange number of items:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-final-2021-03-21/_count?q=*&amp;pretty'
{
&quot;count&quot; : 844,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
</code></pre><ul>
<li>I deleted all indexes and re-created the openrxv-items alias:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{&quot;actions&quot; : [{&quot;add&quot; : { &quot;index&quot; : &quot;openrxv-items-final&quot;, &quot;alias&quot; : &quot;openrxv-items&quot;}}]}'
$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
...
&quot;openrxv-items-temp&quot;: {
&quot;aliases&quot;: {}
},
&quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {
&quot;openrxv-items&quot;: {}
}
}
</code></pre><ul>
<li>Then I started a new harvesting</li>
<li>I switched the Node.js in the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to v12 since v10 will cease to be supported soon
<ul>
<li>I re-deployed DSpace Test (linode26) with Node.js 12 and restarted the server</li>
</ul>
</li>
<li>The AReS harvest finally finished, with 1047 pages of items, but the <code>openrxv-items-final</code> index is empty and the <code>openrxv-items-temp</code> index has a 103,000 items:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty'
{
&quot;count&quot; : 103162,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
</code></pre><ul>
<li>I tried to clone the temp index to the final, but got an error:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-final
{&quot;error&quot;:{&quot;root_cause&quot;:[{&quot;type&quot;:&quot;resource_already_exists_exception&quot;,&quot;reason&quot;:&quot;index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists&quot;,&quot;index_uuid&quot;:&quot;LmxH-rQsTRmTyWex2d8jxw&quot;,&quot;index&quot;:&quot;openrxv-items-final&quot;}],&quot;type&quot;:&quot;resource_already_exists_exception&quot;,&quot;reason&quot;:&quot;index [openrxv-items-final/LmxH-rQsTRmTyWex2d8jxw] already exists&quot;,&quot;index_uuid&quot;:&quot;LmxH-rQsTRmTyWex2d8jxw&quot;,&quot;index&quot;:&quot;openrxv-items-final&quot;},&quot;status&quot;:400}%
</code></pre><ul>
<li>I looked in the Docker logs for Elasticsearch and saw a few memory errors:</li>
</ul>
<pre><code class="language-console" data-lang="console">java.lang.OutOfMemoryError: Java heap space
</code></pre><ul>
<li>According to <code>/usr/share/elasticsearch/config/jvm.options</code> in the Elasticsearch container the default JVM heap is 1g
<ul>
<li>I see the running Java process has <code>-Xms 1g -Xmx 1g</code> in its process invocation so I guess that it must be indeed using 1g</li>
<li>We can <a href="https://www.elastic.co/guide/en/elasticsearch/reference/current/docker.html">change the heap size with the ES_JAVA_OPTS environment variable</a></li>
<li>Or perhaps better, we should <a href="https://www.elastic.co/guide/en/elasticsearch/reference/master/jvm-options.html">use a jvm.options.d file</a> because if you use the environment variable it overrides all other JVM options from the default <code>jvm.options</code></li>
<li>I tried to set memory to 1536m by binding an options file and restarting the container, but it didn&rsquo;t seem to work</li>
<li>Nevertheless, after restarting I see 103,000 items in the Explorer&hellip;</li>
<li>But the indexes are still kinda messed up&hellip; the <code>openrxv-items</code> index is an alias of the wrong index!</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console"> &quot;openrxv-items-final&quot;: {
&quot;aliases&quot;: {}
},
&quot;openrxv-items-temp&quot;: {
&quot;aliases&quot;: {
&quot;openrxv-items&quot;: {}
}
},
</code></pre><h2 id="2021-03-23">2021-03-23</h2>
<ul>
<li>For reference you can also get the Elasticsearch JVM stats from the API:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_nodes/jvm?human' | python -m json.tool
</code></pre><ul>
<li>I re-deployed AReS with 1.5GB of heap using the <code>ES_JAVA_OPTS</code> environment variable
<ul>
<li>It turns out that this <em>is</em> the recommended way to set the heap: <a href="https://www.elastic.co/guide/en/elasticsearch/reference/7.6/jvm-options.html">https://www.elastic.co/guide/en/elasticsearch/reference/7.6/jvm-options.html</a></li>
</ul>
</li>
<li>Then I fixed the aliases to make sure <code>openrxv-items</code> was an alias of <code>openrxv-items-final</code>, similar to how I did a few weeks ago</li>
<li>I re-created the temp index:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -XPUT 'http://localhost:9200/openrxv-items-temp'
</code></pre><!-- raw HTML omitted -->

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@ -17,7 +17,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="404 Page not found"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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@ -10,14 +10,14 @@
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2021-03-14T21:34:07+02:00" />
<meta property="og:updated_time" content="2021-03-17T14:57:45+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>
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<meta property="og:updated_time" content="2021-03-14T21:34:07+02:00" />
<meta property="og:updated_time" content="2021-03-17T14:57:45+02:00" />
<meta name="twitter:card" content="summary"/>
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@ -10,14 +10,14 @@
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-03-14T21:34:07+02:00" />
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<meta name="twitter:card" content="summary"/>
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@ -10,14 +10,14 @@
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-03-17T14:57:45+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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@ -10,14 +10,14 @@
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@ -10,14 +10,14 @@
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@ -18,7 +18,7 @@
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