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Alan Orth 2021-03-04 22:46:05 +02:00
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88
content/posts/2021-02.md
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@ -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
```
<!-- vim: set sw=2 ts=2: -->

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@ -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
<!--more-->
## 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
<!-- vim: set sw=2 ts=2: -->

6
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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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -242,6 +242,8 @@ db.statementpool = true
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -250,8 +252,6 @@ db.statementpool = true
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -264,6 +264,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -272,8 +274,6 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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.
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -200,6 +200,8 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} ; | sor
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -208,8 +210,6 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} ; | sor
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2016-02/index.html
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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;
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -378,6 +378,8 @@ Bitstream: tést señora alimentación.pdf
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -386,8 +388,6 @@ Bitstream: tést señora alimentación.pdf
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -316,6 +316,8 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -324,8 +326,6 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -495,6 +495,8 @@ dspace.log.2016-04-27:7271
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -503,8 +505,6 @@ dspace.log.2016-04-27:7271
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -371,6 +371,8 @@ sys 0m20.540s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -379,8 +381,6 @@ sys 0m20.540s
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -409,6 +409,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -417,8 +419,6 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -325,6 +325,8 @@ discovery.index.authority.ignore-variants=true
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -333,8 +335,6 @@ discovery.index.authority.ignore-variants=true
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -389,6 +389,8 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -397,8 +399,6 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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;
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -606,6 +606,8 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -614,8 +616,6 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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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<meta name="generator" content="Hugo 0.81.0" />
@ -372,6 +372,8 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http:
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -380,8 +382,6 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http:
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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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<meta name="generator" content="Hugo 0.81.0" />
@ -548,6 +548,8 @@ org.dspace.discovery.SearchServiceException: Error executing query
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -556,8 +558,6 @@ org.dspace.discovery.SearchServiceException: Error executing query
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
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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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -784,6 +784,8 @@ $ exit
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -792,8 +794,6 @@ $ exit
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-01/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -369,6 +369,8 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -377,8 +379,6 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-02/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -424,6 +424,8 @@ COPY 1968
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -432,8 +434,6 @@ COPY 1968
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-03/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -355,6 +355,8 @@ $ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.spon
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -363,8 +365,6 @@ $ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.spon
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-04/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -585,6 +585,8 @@ $ gem install compass -v 1.0.3
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -593,8 +595,6 @@ $ gem install compass -v 1.0.3
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-05/index.html
View File

@ -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."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -391,6 +391,8 @@ UPDATE 187
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -399,8 +401,6 @@ UPDATE 187
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-06/index.html
View File

@ -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."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -270,6 +270,8 @@ $ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; [dspace]/bin/dspace impo
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -278,8 +280,6 @@ $ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; [dspace]/bin/dspace impo
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-07/index.html
View File

@ -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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -275,6 +275,8 @@ delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -283,8 +285,6 @@ delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-08/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -517,6 +517,8 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -525,8 +527,6 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-09/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -659,6 +659,8 @@ Cert Status: good
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -667,8 +669,6 @@ Cert Status: good
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-10/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -443,6 +443,8 @@ session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -451,8 +453,6 @@ session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-11/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -944,6 +944,8 @@ $ cat dspace.log.2017-11-28 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | u
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -952,8 +954,6 @@ $ cat dspace.log.2017-11-28 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | u
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2017-12/index.html
View File

@ -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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -783,6 +783,8 @@ DELETE 20
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -791,8 +793,6 @@ DELETE 20
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-01/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1452,6 +1452,8 @@ Catalina:type=Manager,context=/,host=localhost activeSessions 8
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1460,8 +1462,6 @@ Catalina:type=Manager,context=/,host=localhost activeSessions 8
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-02/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1039,6 +1039,8 @@ UPDATE 3
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1047,8 +1049,6 @@ UPDATE 3
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-03/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -585,6 +585,8 @@ Fixed 5 occurences of: GENEBANKS
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -593,8 +595,6 @@ Fixed 5 occurences of: GENEBANKS
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-04/index.html
View File

@ -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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -594,6 +594,8 @@ $ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -602,8 +604,6 @@ $ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-05/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -523,6 +523,8 @@ $ psql -h localhost -U postgres dspacetest
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -531,8 +533,6 @@ $ psql -h localhost -U postgres dspacetest
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-06/index.html
View File

@ -58,7 +58,7 @@ real 74m42.646s
user 8m5.056s
sys 2m7.289s
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -517,6 +517,8 @@ $ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 &gt; map-to-cifor-archive.csv
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -525,8 +527,6 @@ $ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 &gt; map-to-cifor-archive.csv
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-07/index.html
View File

@ -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.
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -569,6 +569,8 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -577,8 +579,6 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-08/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -442,6 +442,8 @@ $ dspace database migrate ignored
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -450,8 +452,6 @@ $ dspace database migrate ignored
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-09/index.html
View File

@ -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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -748,6 +748,8 @@ UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_f
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -756,8 +758,6 @@ UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_f
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-10/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -656,6 +656,8 @@ $ curl -X GET -H &quot;Content-Type: application/json&quot; -H &quot;Accept: app
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -664,8 +666,6 @@ $ curl -X GET -H &quot;Content-Type: application/json&quot; -H &quot;Accept: app
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-11/index.html
View File

@ -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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -553,6 +553,8 @@ $ dspace dsrun org.dspace.eperson.Groomer -a -b 11/27/2016 -d
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -561,8 +563,6 @@ $ dspace dsrun org.dspace.eperson.Groomer -a -b 11/27/2016 -d
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2018-12/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -594,6 +594,8 @@ UPDATE 1
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -602,8 +604,6 @@ UPDATE 1
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-01/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1264,6 +1264,8 @@ identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1272,8 +1274,6 @@ identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-02/index.html
View File

@ -72,7 +72,7 @@ real 0m19.873s
user 0m22.203s
sys 0m1.979s
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1344,6 +1344,8 @@ Please see the DSpace documentation for assistance.
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1352,8 +1354,6 @@ Please see the DSpace documentation for assistance.
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-03/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1208,6 +1208,8 @@ sys 0m2.551s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1216,8 +1218,6 @@ sys 0m2.551s
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-04/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1299,6 +1299,8 @@ UPDATE 14
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1307,8 +1309,6 @@ UPDATE 14
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-05/index.html
View File

@ -48,7 +48,7 @@ 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 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -631,6 +631,8 @@ COPY 64871
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -639,8 +641,6 @@ COPY 64871
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-06/index.html
View File

@ -34,7 +34,7 @@ Run system updates on CGSpace (linode18) and reboot it
Skype with Marie-Angélique and Abenet about CG Core v2
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -317,6 +317,8 @@ UPDATE 2
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -325,8 +327,6 @@ UPDATE 2
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-07/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -554,6 +554,8 @@ issn.validate('1020-3362')
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -562,8 +564,6 @@ issn.validate('1020-3362')
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-08/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -573,6 +573,8 @@ sys 2m27.496s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -581,8 +583,6 @@ sys 2m27.496s
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-09/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -581,6 +581,8 @@ $ csv-metadata-quality -i /tmp/clarisa-institutions.csv -o /tmp/clarisa-institut
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -589,8 +591,6 @@ $ csv-metadata-quality -i /tmp/clarisa-institutions.csv -o /tmp/clarisa-institut
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-10/index.html
View File

@ -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."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -385,6 +385,8 @@ $ dspace import -a -c 10568/104057 -e fuu@cgiar.org -m 2019-10-15-Bioversity.map
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -393,8 +395,6 @@ $ dspace import -a -c 10568/104057 -e fuu@cgiar.org -m 2019-10-15-Bioversity.map
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-11/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -692,6 +692,8 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -700,8 +702,6 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2019-12/index.html
View File

@ -46,7 +46,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# dpkg -C
# reboot
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -404,6 +404,8 @@ UPDATE 1
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -412,8 +414,6 @@ UPDATE 1
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-01/index.html
View File

@ -56,7 +56,7 @@ I tweeted the CGSpace repository link
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -604,6 +604,8 @@ COPY 2900
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -612,8 +614,6 @@ COPY 2900
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-02/index.html
View File

@ -38,7 +38,7 @@ The code finally builds and runs with a fresh install
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1275,6 +1275,8 @@ Moving: 21993 into core statistics-2019
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1283,8 +1285,6 @@ Moving: 21993 into core statistics-2019
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-03/index.html
View File

@ -42,7 +42,7 @@ You need to download this into the DSpace 6.x source and compile it
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -484,6 +484,8 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -492,8 +494,6 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-04/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -658,6 +658,8 @@ $ psql -c 'select * from pg_stat_activity' | wc -l
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -666,8 +668,6 @@ $ psql -c 'select * from pg_stat_activity' | wc -l
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-05/index.html
View File

@ -34,7 +34,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -477,6 +477,8 @@ Caused by: java.lang.NullPointerException
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -485,8 +487,6 @@ Caused by: java.lang.NullPointerException
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-06/index.html
View File

@ -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:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -811,6 +811,8 @@ $ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -819,8 +821,6 @@ $ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-07/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1142,6 +1142,8 @@ Fixed 4 occurences of: Muloi, D.M.
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1150,8 +1152,6 @@ Fixed 4 occurences of: Muloi, D.M.
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-08/index.html
View File

@ -36,7 +36,7 @@ It is class based so I can easily add support for other vocabularies, and the te
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -798,6 +798,8 @@ $ grep -c added /tmp/2020-08-27-countrycodetagger.log
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -806,8 +808,6 @@ $ grep -c added /tmp/2020-08-27-countrycodetagger.log
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-09/index.html
View File

@ -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
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -717,6 +717,8 @@ solr_query_params = {
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -725,8 +727,6 @@ solr_query_params = {
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-10/index.html
View File

@ -44,7 +44,7 @@ During the FlywayDB migration I got an error:
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -1241,6 +1241,8 @@ $ ./delete-metadata-values.py -i 2020-10-31-delete-74-sponsors.csv -db dspace -u
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -1249,8 +1251,6 @@ $ ./delete-metadata-values.py -i 2020-10-31-delete-74-sponsors.csv -db dspace -u
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-11/index.html
View File

@ -32,7 +32,7 @@ So far we&rsquo;ve spent at least fifty hours to process the statistics and stat
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -731,6 +731,8 @@ $ ./fix-metadata-values.py -i 2020-11-30-fix-hung-orcid.csv -db dspace63 -u dspa
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -739,8 +741,6 @@ $ ./fix-metadata-values.py -i 2020-11-30-fix-hung-orcid.csv -db dspace63 -u dspa
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2020-12/index.html
View File

@ -36,7 +36,7 @@ I started processing those (about 411,000 records):
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -869,6 +869,8 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-items-2020-12-29?pretty'
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -877,8 +879,6 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-items-2020-12-29?pretty'
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/2021-01/index.html
View File

@ -50,7 +50,7 @@ For example, this item has 51 views on CGSpace, but 0 on AReS
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -688,6 +688,8 @@ java.lang.IllegalArgumentException: Invalid character found in the request targe
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -696,8 +698,6 @@ java.lang.IllegalArgumentException: Invalid character found in the request targe
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

103
docs/2021-02/index.html
View File

@ -32,7 +32,7 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-02/" />
<meta property="article:published_time" content="2021-02-01T10:13:54+02:00" />
<meta property="article:modified_time" content="2021-02-21T20:37:27+02:00" />
<meta property="article:modified_time" content="2021-02-24T09:21:07+02:00" />
@ -60,7 +60,7 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
}
}
"/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -70,9 +70,9 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
"@type": "BlogPosting",
"headline": "February, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-02/",
"wordCount": "3754",
"wordCount": "4170",
"datePublished": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-02-21T20:37:27+02:00",
"dateModified": "2021-02-24T09:21:07+02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -779,7 +779,7 @@ UPDATE 18659
</ul>
<pre><code class="language-console" data-lang="console">$ dspace metadata-import -f /tmp/0.csv
</code></pre><ul>
<li>It took FOREVER to import each file&hellip; like several hours. MY GOD DSpace 6 is slow.</li>
<li>It took FOREVER to import each file&hellip; like several hours <em>each</em>. MY GOD DSpace 6 is slow.</li>
<li>Help Dominique Perera debug some issues with the WordPress DSpace importer plugin from Macaroni Bros
<ul>
<li>She is not seeing the community list for CGSpace, and I see weird requests like this in the logs:</li>
@ -791,7 +791,94 @@ UPDATE 18659
</code></pre><ul>
<li>The first request is OK, but the second one is malformed for sure</li>
</ul>
<!-- raw HTML omitted -->
<h2 id="2021-02-24">2021-02-24</h2>
<ul>
<li>Export a list of journals for Peter to look through:</li>
</ul>
<pre><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &quot;cg.journal&quot;, 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
</code></pre><ul>
<li>Start a fresh harvesting on AReS because Udana mapped some items today and wants to include them in his report:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
# start indexing in AReS
</code></pre><ul>
<li>Also, I want to include the new series name/number cleanups so it&rsquo;s not a total waste of time</li>
</ul>
<h2 id="2021-02-25">2021-02-25</h2>
<ul>
<li>Hmm the AReS harvest last night seems to have finished successfully, but the number of items is less than I was expecting:</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; : 99546,
&quot;_shards&quot; : {
&quot;total&quot; : 1,
&quot;successful&quot; : 1,
&quot;skipped&quot; : 0,
&quot;failed&quot; : 0
}
}
</code></pre><ul>
<li>The current items index has 101380 items&hellip; I wonder what happened
<ul>
<li>I started a new indexing</li>
</ul>
</li>
</ul>
<h2 id="2021-02-26">2021-02-26</h2>
<ul>
<li>Last night&rsquo;s indexing was more successful, there are now 101479 items in the index</li>
<li>Yesterday Yousef sent a <a href="https://github.com/ilri/OpenRXV/pull/77/">pull request</a> for the next/previous buttons on OpenRXV
<ul>
<li>I tested it this morning and it seems to be working</li>
</ul>
</li>
</ul>
<h2 id="2021-02-28">2021-02-28</h2>
<ul>
<li>Abenet asked me to import seventy-three records for CRP Forests, Trees and Agroforestry
<ul>
<li>I checked them briefly and found that there were thirty+ journal articles, and none of them had <code>cg.journal</code>, <code>cg.volume</code>, <code>cg.issue</code>, or <code>dcterms.license</code> so I spent a little time adding them</li>
<li>I used a GREL expression to extract the journal volume and issue from the citation into new columns:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/\(.*\)/,&quot;&quot;)
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,&quot;$1&quot;)
</code></pre><ul>
<li>This <code>value.partition</code> was new to me&hellip; and it took me a bit of time to figure out whether I needed to escape the parentheses in the issue number or not (no) and how to reference a capture group with <code>value.replace</code></li>
<li>I tried to check the 1095 CIFOR records from last week for duplicates on DSpace Test, but the page says &ldquo;Processing&rdquo; and never loads
<ul>
<li>I don&rsquo;t see any errors in the logs, but there are two jQuery errors in the browser console</li>
<li>I filed <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=934">an issue</a> with Atmire</li>
</ul>
</li>
<li>Upload twelve items to CGSpace for Peter</li>
<li>Niroshini from IWMI is still having issues adding WLE subjects to items during the metadata review step in the workflow</li>
<li>It seems the BatchEditConsumer log spam is gone since I applied <a href="https://github.com/ilri/DSpace/pull/462">Atmire&rsquo;s patch</a></li>
</ul>
<pre><code class="language-console" data-lang="console">$ 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
</code></pre><!-- raw HTML omitted -->
@ -812,6 +899,8 @@ UPDATE 18659
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -820,8 +909,6 @@ UPDATE 18659
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

304
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@ -0,0 +1,304 @@
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Discuss some OpenRXV issues with Abdullah from CodeObia
He&rsquo;s trying to work on the DSpace 6&#43; metadata schema autoimport using the DSpace 6&#43; REST API
Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies
" />
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Discuss some OpenRXV issues with Abdullah from CodeObia
He&rsquo;s trying to work on the DSpace 6&#43; metadata schema autoimport using the DSpace 6&#43; REST API
Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-03/">March, 2021</a></h2>
<p class="blog-post-meta">
<time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-03-01">2021-03-01</h2>
<ul>
<li>Discuss some OpenRXV issues with Abdullah from CodeObia
<ul>
<li>He&rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
</ul>
</li>
</ul>
<h2 id="2021-03-02">2021-03-02</h2>
<ul>
<li>I fixed three build and runtime issues in OpenRXV:
<ul>
<li><a href="https://github.com/ilri/OpenRXV/pull/80">fix highcharts-angular and ngx-tour-core build</a></li>
<li><a href="https://github.com/ilri/OpenRXV/pull/82">frontend/package.json: Pin @types/ramda at 0.27.34</a></li>
</ul>
</li>
<li>Then I merged a few fixes that Abdullah had worked on last week</li>
</ul>
<h2 id="2021-03-03">2021-03-03</h2>
<ul>
<li>I <a href="https://github.com/ilri/OpenRXV/issues/83">fixed another frontend build warning on OpenRXV</a></li>
<li>Then I <a href="https://github.com/ilri/OpenRXV/pull/84">updated the frontend container to use Node.js 12 and Ubuntu 20.04</a></li>
<li>Also, I <a href="https://github.com/ilri/OpenRXV/pull/85">added a GitHub Actions workflow to build the frontend</a></li>
<li>I did some testing of Abdullah&rsquo;s patch for the values mapping search on OpenRXV
<ul>
<li>It still doesn&rsquo;t work with multi-word values, so I recorded a video with wf-recorder and uploaded it to <a href="https://github.com/ilri/OpenRXV/issues/43">the issue</a> for him to investigate</li>
</ul>
</li>
</ul>
<h2 id="2021-03-04">2021-03-04</h2>
<ul>
<li>Peter is having issues with the workflow since yesterday
<ul>
<li>I looked at the Munin stats and see a high number of database locks since yesterday</li>
</ul>
</li>
</ul>
<p><img src="/cgspace-notes/2021/03/postgres_locks_ALL-week.png" alt="PostgreSQL locks week">
<img src="/cgspace-notes/2021/03/postgres_connections_cgspace-week.png" alt="PostgreSQL connections week"></p>
<ul>
<li>I looked at the number of connections in PostgreSQL and it&rsquo;s definitely high again:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1020
</code></pre><ul>
<li>I reported it to Atmire to take a look, on the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=851">same issue</a> we had been tracking this before</li>
<li>Abenet asked me to add a new ORCID for ILRI staff member Zoe Campbell</li>
<li>I added it to the controlled vocabulary and then tagged her existing items on CGSpace using my <code>add-orcid-identifier.py</code> script:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ cat 2021-03-04-add-zoe-campbell-orcid.csv
dc.contributor.author,cg.creator.identifier
&quot;Campbell, Zoë&quot;,&quot;Zoe Campbell: 0000-0002-4759-9976&quot;
&quot;Campbell, Zoe A.&quot;,&quot;Zoe Campbell: 0000-0002-4759-9976&quot;
$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p 'fuuu'
</code></pre><ul>
<li>I still need to do cleanup on the journal articles metadata
<ul>
<li>Peter sent me some cleanups but I can&rsquo;t use them in the search/replace format he gave</li>
<li>I think it&rsquo;s better to export the metadata values with IDs and import cleaned up ones as CSV</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT dspace_object_id AS id, text_value as &quot;cg.journal&quot; 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
</code></pre><ul>
<li>I used OpenRefine to remove all journal values that didn&rsquo;t have one of these values: ; ( )
<ul>
<li>Then I cloned the <code>cg.journal</code> field to <code>cg.volume</code> and <code>cg.issue</code></li>
<li>I used some GREL expressions like these to extract the journal name, volume, and issue:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">value.partition(';')[0].trim() # to get journal names
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,&quot;$1&quot;) # to get journal volumes
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,&quot;$1&quot;) # to get journal issues
</code></pre><ul>
<li>Then I uploaded the changes to CGSpace using <code>dspace metadata-import</code></li>
<li>Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
<ul>
<li>The error was &ldquo;Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e &hellip;&rdquo;</li>
<li>I searched the DSpace issue tracker and found several issues reporting this:
<ul>
<li><a href="https://jira.lyrasis.org/browse/DS-3985">DS-3985 Delete item fails</a></li>
<li><a href="https://jira.lyrasis.org/browse/DS-4004">DS-4004 Authorization denied Exception when trying to delete permanently an item, collection or community as a non-Admin user</a></li>
<li><a href="https://jira.lyrasis.org/browse/DS-4297">DS-4297 Authorization error when trying to delete item by submitter/administrator</a></li>
</ul>
</li>
<li>The issue is apparently with non-admin users who are in the admin and submit groups of the owning collection&hellip;</li>
<li>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&rsquo;s admin and submit groups, exactly as the issue described</li>
<li>I added a comment about our issue to <a href="https://jira.lyrasis.org/browse/DS-4297">DS-4297</a></li>
</ul>
</li>
<li>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&rsquo;s submissions
<ul>
<li>I edited Udana&rsquo;s submission to CGSpace:
<ul>
<li>corrected the title</li>
<li>added language English</li>
<li>changed the link to the external item page instead of PDF</li>
<li>added SDGs from the external item page</li>
<li>added AGROVOC subjects from the external item page</li>
<li>added pagination (extent)</li>
<li>changed the license to &ldquo;other&rdquo; because CC-BY-NC-ND is not printed anywhere in the PDF or external item page</li>
</ul>
</li>
</ul>
</li>
</ul>
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<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
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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."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -95,6 +95,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -103,8 +105,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

10
docs/categories/index.html
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@ -10,14 +10,14 @@
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<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 0.80.0" />
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@ -84,7 +84,7 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/categories/notes/">Notes</a></h2>
<p class="blog-post-meta"><time datetime="2021-02-01T10:13:54+02:00">Mon Feb 01, 2021</time> by Alan Orth</p>
<p class="blog-post-meta"><time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time> by Alan Orth</p>
</header>
<a href='https://alanorth.github.io/cgspace-notes/categories/notes/'>Read more →</a>
@ -108,6 +108,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -116,8 +118,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

4
docs/categories/index.xml
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@ -6,11 +6,11 @@
<description>Recent content in Categories on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Mon, 01 Feb 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="self" type="application/rss+xml" />
<lastBuildDate>Mon, 01 Mar 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>Notes</title>
<link>https://alanorth.github.io/cgspace-notes/categories/notes/</link>
<pubDate>Mon, 01 Feb 2021 10:13:54 +0200</pubDate>
<pubDate>Mon, 01 Mar 2021 10:13:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/categories/notes/</guid>
<description></description>

61
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2021-03-01T10:13:54+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."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -81,6 +81,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-03/">March, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-03-01">2021-03-01</h2>
<ul>
<li>Discuss some OpenRXV issues with Abdullah from CodeObia
<ul>
<li>He&rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2021-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
@ -344,33 +370,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -395,6 +394,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -403,8 +404,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

19
docs/categories/notes/index.xml
View File

@ -6,7 +6,24 @@
<description>Recent content in Notes on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Mon, 01 Feb 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="self" type="application/rss+xml" />
<lastBuildDate>Mon, 01 Mar 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>March, 2021</title>
<link>https://alanorth.github.io/cgspace-notes/2021-03/</link>
<pubDate>Mon, 01 Mar 2021 10:13:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2021-03/</guid>
<description>&lt;h2 id=&#34;2021-03-01&#34;&gt;2021-03-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Discuss some OpenRXV issues with Abdullah from CodeObia
&lt;ul&gt;
&lt;li&gt;He&amp;rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API&lt;/li&gt;
&lt;li&gt;Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ul&gt;</description>
</item>
<item>
<title>February, 2021</title>
<link>https://alanorth.github.io/cgspace-notes/2021-02/</link>

80
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -81,6 +81,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
@ -343,51 +370,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-09/">September, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-09-01T10:17:51+03:00">Sun Sep 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-09-01">2019-09-01</h2>
<ul>
<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
</ul>
<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
440 17.58.101.255
441 157.55.39.101
485 207.46.13.43
728 169.60.128.125
730 207.46.13.108
758 157.55.39.9
808 66.160.140.179
814 207.46.13.212
2472 163.172.71.23
6092 3.94.211.189
# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
33 2a01:7e00::f03c:91ff:fe16:fcb
57 3.83.192.124
57 3.87.77.25
57 54.82.1.8
822 2a01:9cc0:47:1:1a:4:0:2
1223 45.5.184.72
1633 172.104.229.92
5112 205.186.128.185
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-09/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/" rel="prev" role="button">Previous page</a>
@ -412,6 +394,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -420,8 +404,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

80
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -81,6 +81,51 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-09/">September, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-09-01T10:17:51+03:00">Sun Sep 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-09-01">2019-09-01</h2>
<ul>
<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
</ul>
<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
440 17.58.101.255
441 157.55.39.101
485 207.46.13.43
728 169.60.128.125
730 207.46.13.108
758 157.55.39.9
808 66.160.140.179
814 207.46.13.212
2472 163.172.71.23
6092 3.94.211.189
# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
33 2a01:7e00::f03c:91ff:fe16:fcb
57 3.83.192.124
57 3.87.77.25
57 54.82.1.8
822 2a01:9cc0:47:1:1a:4:0:2
1223 45.5.184.72
1633 172.104.229.92
5112 205.186.128.185
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-09/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-08/">August, 2019</a></h2>
@ -378,33 +423,6 @@ sys 0m1.979s
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-11-01">2018-11-01</h2>
<ul>
<li>Finalize AReS Phase I and Phase II ToRs</li>
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
</ul>
<h2 id="2018-11-03">2018-11-03</h2>
<ul>
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
<li>Today these are the top 10 IPs:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/2/" rel="prev" role="button">Previous page</a>
@ -429,6 +447,8 @@ sys 0m1.979s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -437,8 +457,6 @@ sys 0m1.979s
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

119
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+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."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -81,6 +81,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-11-01">2018-11-01</h2>
<ul>
<li>Finalize AReS Phase I and Phase II ToRs</li>
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
</ul>
<h2 id="2018-11-03">2018-11-03</h2>
<ul>
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
<li>Today these are the top 10 IPs:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-10/">October, 2018</a></h2>
@ -318,90 +345,6 @@ sys 2m7.289s
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-01-02">2018-01-02</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre><ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32.
</code></pre><ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre><ul>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/3/" rel="prev" role="button">Previous page</a>
@ -426,6 +369,8 @@ dspace.log.2018-01-02:34
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -434,8 +379,6 @@ dspace.log.2018-01-02:34
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

92
docs/categories/notes/page/5/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+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."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -81,6 +81,90 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-01-02">2018-01-02</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre><ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32.
</code></pre><ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre><ul>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-12/">December, 2017</a></h2>
@ -207,6 +291,8 @@ COPY 54701
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -215,8 +301,6 @@ COPY 54701
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/cgiar-library-migration/index.html
View File

@ -18,7 +18,7 @@
<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 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -282,6 +282,8 @@ dspace=# select setval('handle_seq',86873);
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -290,8 +292,6 @@ dspace=# select setval('handle_seq',86873);
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/cgspace-cgcorev2-migration/index.html
View File

@ -18,7 +18,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace CG Core v2 Migration"/>
<meta name="twitter:description" content="Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -462,6 +462,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -470,8 +472,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

6
docs/cgspace-dspace6-upgrade/index.html
View File

@ -18,7 +18,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace DSpace 6 Upgrade"/>
<meta name="twitter:description" content="Documenting the DSpace 6 upgrade."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -471,6 +471,8 @@ $ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -479,8 +481,6 @@ $ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

63
docs/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-03/">March, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-03-01">2021-03-01</h2>
<ul>
<li>Discuss some OpenRXV issues with Abdullah from CodeObia
<ul>
<li>He&rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2021-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
@ -359,33 +385,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -410,6 +409,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -418,8 +419,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

19
docs/index.xml
View File

@ -6,7 +6,24 @@
<description>Recent content on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Mon, 01 Feb 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="self" type="application/rss+xml" />
<lastBuildDate>Mon, 01 Mar 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>March, 2021</title>
<link>https://alanorth.github.io/cgspace-notes/2021-03/</link>
<pubDate>Mon, 01 Mar 2021 10:13:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2021-03/</guid>
<description>&lt;h2 id=&#34;2021-03-01&#34;&gt;2021-03-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Discuss some OpenRXV issues with Abdullah from CodeObia
&lt;ul&gt;
&lt;li&gt;He&amp;rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API&lt;/li&gt;
&lt;li&gt;Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ul&gt;</description>
</item>
<item>
<title>February, 2021</title>
<link>https://alanorth.github.io/cgspace-notes/2021-02/</link>

82
docs/page/2/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
@ -358,51 +385,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-09/">September, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-09-01T10:17:51+03:00">Sun Sep 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-09-01">2019-09-01</h2>
<ul>
<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
</ul>
<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
440 17.58.101.255
441 157.55.39.101
485 207.46.13.43
728 169.60.128.125
730 207.46.13.108
758 157.55.39.9
808 66.160.140.179
814 207.46.13.212
2472 163.172.71.23
6092 3.94.211.189
# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
33 2a01:7e00::f03c:91ff:fe16:fcb
57 3.83.192.124
57 3.87.77.25
57 54.82.1.8
822 2a01:9cc0:47:1:1a:4:0:2
1223 45.5.184.72
1633 172.104.229.92
5112 205.186.128.185
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-09/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/" rel="prev" role="button">Previous page</a>
@ -427,6 +409,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -435,8 +419,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

82
docs/page/3/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,51 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-09/">September, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-09-01T10:17:51+03:00">Sun Sep 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-09-01">2019-09-01</h2>
<ul>
<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
</ul>
<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
440 17.58.101.255
441 157.55.39.101
485 207.46.13.43
728 169.60.128.125
730 207.46.13.108
758 157.55.39.9
808 66.160.140.179
814 207.46.13.212
2472 163.172.71.23
6092 3.94.211.189
# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
33 2a01:7e00::f03c:91ff:fe16:fcb
57 3.83.192.124
57 3.87.77.25
57 54.82.1.8
822 2a01:9cc0:47:1:1a:4:0:2
1223 45.5.184.72
1633 172.104.229.92
5112 205.186.128.185
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-09/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-08/">August, 2019</a></h2>
@ -393,33 +438,6 @@ sys 0m1.979s
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-11-01">2018-11-01</h2>
<ul>
<li>Finalize AReS Phase I and Phase II ToRs</li>
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
</ul>
<h2 id="2018-11-03">2018-11-03</h2>
<ul>
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
<li>Today these are the top 10 IPs:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/2/" rel="prev" role="button">Previous page</a>
@ -444,6 +462,8 @@ sys 0m1.979s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -452,8 +472,6 @@ sys 0m1.979s
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

121
docs/page/4/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-11-01">2018-11-01</h2>
<ul>
<li>Finalize AReS Phase I and Phase II ToRs</li>
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
</ul>
<h2 id="2018-11-03">2018-11-03</h2>
<ul>
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
<li>Today these are the top 10 IPs:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-10/">October, 2018</a></h2>
@ -333,90 +360,6 @@ sys 2m7.289s
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-01-02">2018-01-02</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre><ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32.
</code></pre><ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre><ul>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/3/" rel="prev" role="button">Previous page</a>
@ -441,6 +384,8 @@ dspace.log.2018-01-02:34
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -449,8 +394,6 @@ dspace.log.2018-01-02:34
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

123
docs/page/5/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,90 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-01-02">2018-01-02</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre><ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32.
</code></pre><ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre><ul>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-12/">December, 2017</a></h2>
@ -325,35 +409,6 @@ COPY 54701
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-04/">April, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-04-02T17:08:52+02:00">Sun Apr 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-04-02">2017-04-02</h2>
<ul>
<li>Merge one change to CCAFS flagships that I had forgotten to remove last month (&ldquo;MANAGING CLIMATE RISK&rdquo;): <a href="https://github.com/ilri/DSpace/pull/317">https://github.com/ilri/DSpace/pull/317</a></li>
<li>Quick proof-of-concept hack to add <code>dc.rights</code> to the input form, including some inline instructions/hints:</li>
</ul>
<p><img src="/cgspace-notes/2017/04/dc-rights.png" alt="dc.rights in the submission form"></p>
<ul>
<li>Remove redundant/duplicate text in the DSpace submission license</li>
<li>Testing the CMYK patch on a collection with 650 items:</li>
</ul>
<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/4/" rel="prev" role="button">Previous page</a>
@ -378,6 +433,8 @@ COPY 54701
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -386,8 +443,6 @@ COPY 54701
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

65
docs/page/6/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,35 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-04/">April, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-04-02T17:08:52+02:00">Sun Apr 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-04-02">2017-04-02</h2>
<ul>
<li>Merge one change to CCAFS flagships that I had forgotten to remove last month (&ldquo;MANAGING CLIMATE RISK&rdquo;): <a href="https://github.com/ilri/DSpace/pull/317">https://github.com/ilri/DSpace/pull/317</a></li>
<li>Quick proof-of-concept hack to add <code>dc.rights</code> to the input form, including some inline instructions/hints:</li>
</ul>
<p><img src="/cgspace-notes/2017/04/dc-rights.png" alt="dc.rights in the submission form"></p>
<ul>
<li>Remove redundant/duplicate text in the DSpace submission license</li>
<li>Testing the CMYK patch on a collection with 650 items:</li>
</ul>
<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-03/">March, 2017</a></h2>
@ -359,32 +388,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-06/">June, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-06-01T10:53:00+03:00">Wed Jun 01, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
<li>After reading the <a href="https://www.oclc.org/support/services/contentdm/help/server-admin-help/oai-support.en.html">ContentDM documentation</a> I found IFPRI&rsquo;s OAI endpoint: <a href="http://ebrary.ifpri.org/oai/oai.php">http://ebrary.ifpri.org/oai/oai.php</a></li>
<li>After reading the <a href="https://www.openarchives.org/OAI/openarchivesprotocol.html">OAI documentation</a> and testing with an <a href="http://validator.oaipmh.com/">OAI validator</a> I found out how to get their publications</li>
<li>This is their publications set: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc">http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc</a></li>
<li>You can see the others by using the OAI <code>ListSets</code> verb: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListSets">http://ebrary.ifpri.org/oai/oai.php?verb=ListSets</a></li>
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/5/" rel="prev" role="button">Previous page</a>
@ -409,6 +412,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -417,8 +422,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

36
docs/page/7/index.html
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-06/">June, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-06-01T10:53:00+03:00">Wed Jun 01, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
<li>After reading the <a href="https://www.oclc.org/support/services/contentdm/help/server-admin-help/oai-support.en.html">ContentDM documentation</a> I found IFPRI&rsquo;s OAI endpoint: <a href="http://ebrary.ifpri.org/oai/oai.php">http://ebrary.ifpri.org/oai/oai.php</a></li>
<li>After reading the <a href="https://www.openarchives.org/OAI/openarchivesprotocol.html">OAI documentation</a> and testing with an <a href="http://validator.oaipmh.com/">OAI validator</a> I found out how to get their publications</li>
<li>This is their publications set: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc">http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc</a></li>
<li>You can see the others by using the OAI <code>ListSets</code> verb: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListSets">http://ebrary.ifpri.org/oai/oai.php?verb=ListSets</a></li>
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-05/">May, 2016</a></h2>
@ -297,6 +323,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -305,8 +333,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

63
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-03/">March, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-03-01">2021-03-01</h2>
<ul>
<li>Discuss some OpenRXV issues with Abdullah from CodeObia
<ul>
<li>He&rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2021-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
@ -359,33 +385,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -410,6 +409,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -418,8 +419,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

19
docs/posts/index.xml
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@ -6,7 +6,24 @@
<description>Recent content in Posts on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Mon, 01 Feb 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="self" type="application/rss+xml" />
<lastBuildDate>Mon, 01 Mar 2021 10:13:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>March, 2021</title>
<link>https://alanorth.github.io/cgspace-notes/2021-03/</link>
<pubDate>Mon, 01 Mar 2021 10:13:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2021-03/</guid>
<description>&lt;h2 id=&#34;2021-03-01&#34;&gt;2021-03-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Discuss some OpenRXV issues with Abdullah from CodeObia
&lt;ul&gt;
&lt;li&gt;He&amp;rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API&lt;/li&gt;
&lt;li&gt;Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ul&gt;</description>
</item>
<item>
<title>February, 2021</title>
<link>https://alanorth.github.io/cgspace-notes/2021-02/</link>

82
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
@ -358,51 +385,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-09/">September, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-09-01T10:17:51+03:00">Sun Sep 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-09-01">2019-09-01</h2>
<ul>
<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
</ul>
<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
440 17.58.101.255
441 157.55.39.101
485 207.46.13.43
728 169.60.128.125
730 207.46.13.108
758 157.55.39.9
808 66.160.140.179
814 207.46.13.212
2472 163.172.71.23
6092 3.94.211.189
# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
33 2a01:7e00::f03c:91ff:fe16:fcb
57 3.83.192.124
57 3.87.77.25
57 54.82.1.8
822 2a01:9cc0:47:1:1a:4:0:2
1223 45.5.184.72
1633 172.104.229.92
5112 205.186.128.185
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-09/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/" rel="prev" role="button">Previous page</a>
@ -427,6 +409,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -435,8 +419,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

82
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,51 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-09/">September, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-09-01T10:17:51+03:00">Sun Sep 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-09-01">2019-09-01</h2>
<ul>
<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
</ul>
<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
440 17.58.101.255
441 157.55.39.101
485 207.46.13.43
728 169.60.128.125
730 207.46.13.108
758 157.55.39.9
808 66.160.140.179
814 207.46.13.212
2472 163.172.71.23
6092 3.94.211.189
# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
33 2a01:7e00::f03c:91ff:fe16:fcb
57 3.83.192.124
57 3.87.77.25
57 54.82.1.8
822 2a01:9cc0:47:1:1a:4:0:2
1223 45.5.184.72
1633 172.104.229.92
5112 205.186.128.185
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-09/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-08/">August, 2019</a></h2>
@ -393,33 +438,6 @@ sys 0m1.979s
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-11-01">2018-11-01</h2>
<ul>
<li>Finalize AReS Phase I and Phase II ToRs</li>
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
</ul>
<h2 id="2018-11-03">2018-11-03</h2>
<ul>
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
<li>Today these are the top 10 IPs:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/2/" rel="prev" role="button">Previous page</a>
@ -444,6 +462,8 @@ sys 0m1.979s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -452,8 +472,6 @@ sys 0m1.979s
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

121
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@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-11-01">2018-11-01</h2>
<ul>
<li>Finalize AReS Phase I and Phase II ToRs</li>
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
</ul>
<h2 id="2018-11-03">2018-11-03</h2>
<ul>
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
<li>Today these are the top 10 IPs:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-10/">October, 2018</a></h2>
@ -333,90 +360,6 @@ sys 2m7.289s
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-01-02">2018-01-02</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre><ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32.
</code></pre><ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre><ul>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/3/" rel="prev" role="button">Previous page</a>
@ -441,6 +384,8 @@ dspace.log.2018-01-02:34
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -449,8 +394,6 @@ dspace.log.2018-01-02:34
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

123
docs/posts/page/5/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,90 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-01-02">2018-01-02</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre><ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32.
</code></pre><ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre><ul>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-12/">December, 2017</a></h2>
@ -325,35 +409,6 @@ COPY 54701
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-04/">April, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-04-02T17:08:52+02:00">Sun Apr 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-04-02">2017-04-02</h2>
<ul>
<li>Merge one change to CCAFS flagships that I had forgotten to remove last month (&ldquo;MANAGING CLIMATE RISK&rdquo;): <a href="https://github.com/ilri/DSpace/pull/317">https://github.com/ilri/DSpace/pull/317</a></li>
<li>Quick proof-of-concept hack to add <code>dc.rights</code> to the input form, including some inline instructions/hints:</li>
</ul>
<p><img src="/cgspace-notes/2017/04/dc-rights.png" alt="dc.rights in the submission form"></p>
<ul>
<li>Remove redundant/duplicate text in the DSpace submission license</li>
<li>Testing the CMYK patch on a collection with 650 items:</li>
</ul>
<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/4/" rel="prev" role="button">Previous page</a>
@ -378,6 +433,8 @@ COPY 54701
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -386,8 +443,6 @@ COPY 54701
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

65
docs/posts/page/6/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,35 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-04/">April, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-04-02T17:08:52+02:00">Sun Apr 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-04-02">2017-04-02</h2>
<ul>
<li>Merge one change to CCAFS flagships that I had forgotten to remove last month (&ldquo;MANAGING CLIMATE RISK&rdquo;): <a href="https://github.com/ilri/DSpace/pull/317">https://github.com/ilri/DSpace/pull/317</a></li>
<li>Quick proof-of-concept hack to add <code>dc.rights</code> to the input form, including some inline instructions/hints:</li>
</ul>
<p><img src="/cgspace-notes/2017/04/dc-rights.png" alt="dc.rights in the submission form"></p>
<ul>
<li>Remove redundant/duplicate text in the DSpace submission license</li>
<li>Testing the CMYK patch on a collection with 650 items:</li>
</ul>
<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-03/">March, 2017</a></h2>
@ -359,32 +388,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-06/">June, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-06-01T10:53:00+03:00">Wed Jun 01, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
<li>After reading the <a href="https://www.oclc.org/support/services/contentdm/help/server-admin-help/oai-support.en.html">ContentDM documentation</a> I found IFPRI&rsquo;s OAI endpoint: <a href="http://ebrary.ifpri.org/oai/oai.php">http://ebrary.ifpri.org/oai/oai.php</a></li>
<li>After reading the <a href="https://www.openarchives.org/OAI/openarchivesprotocol.html">OAI documentation</a> and testing with an <a href="http://validator.oaipmh.com/">OAI validator</a> I found out how to get their publications</li>
<li>This is their publications set: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc">http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc</a></li>
<li>You can see the others by using the OAI <code>ListSets</code> verb: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListSets">http://ebrary.ifpri.org/oai/oai.php?verb=ListSets</a></li>
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/5/" rel="prev" role="button">Previous page</a>
@ -409,6 +412,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -417,8 +422,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
</ol>
</section>

36
docs/posts/page/7/index.html
View File

@ -10,14 +10,14 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2021-02-21T20:37:27+02:00" />
<meta property="og:updated_time" content="2021-03-01T10:13:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.80.0" />
<meta name="generator" content="Hugo 0.81.0" />
@ -31,7 +31,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2021-02-01T10:13:54+02:00",
"dateModified": "2021-03-01T10:13:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -96,6 +96,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-06/">June, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-06-01T10:53:00+03:00">Wed Jun 01, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
<li>After reading the <a href="https://www.oclc.org/support/services/contentdm/help/server-admin-help/oai-support.en.html">ContentDM documentation</a> I found IFPRI&rsquo;s OAI endpoint: <a href="http://ebrary.ifpri.org/oai/oai.php">http://ebrary.ifpri.org/oai/oai.php</a></li>
<li>After reading the <a href="https://www.openarchives.org/OAI/openarchivesprotocol.html">OAI documentation</a> and testing with an <a href="http://validator.oaipmh.com/">OAI validator</a> I found out how to get their publications</li>
<li>This is their publications set: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc">http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc</a></li>
<li>You can see the others by using the OAI <code>ListSets</code> verb: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListSets">http://ebrary.ifpri.org/oai/oai.php?verb=ListSets</a></li>
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-05/">May, 2016</a></h2>
@ -297,6 +323,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
@ -305,8 +333,6 @@
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
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<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
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<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
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