cgspace-notes/content/posts/2018-08.md

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2018-08-01 11:49:05 +02:00
---
title: "August, 2018"
date: 2018-08-01T11:52:54+03:00
author: "Alan Orth"
tags: ["Notes"]
---
## 2018-08-01
- DSpace Test had crashed at some point yesterday morning and I see the following in `dmesg`:
```
[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
```
- Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight
- From the DSpace log I see that eventually Solr stopped responding, so I guess the `java` process that was OOM killed above was Tomcat's
- I'm not sure why Tomcat didn't crash with an OutOfMemoryError...
- Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core
- The server only has 8GB of RAM so we'll eventually need to upgrade to a larger one because we'll start starving the OS, PostgreSQL, and command line batch processes
- I ran all system updates on DSpace Test and rebooted it
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2018-08-01 16:24:49 +02:00
- I started looking over the latest round of IITA batch records from Sisay on DSpace Test: [IITA July_30](https://dspacetest.cgiar.org/handle/10568/103250)
- incorrect authorship types
- dozens of inconsistencies, spelling mistakes, and white space in author affiliations
- minor issues in countries (California is not a country)
- minor issues in IITA subjects, ISBNs, languages, and AGROVOC subjects
2018-08-02 13:29:59 +02:00
## 2018-08-02
- DSpace Test crashed again and I don't see the only error I see is this in `dmesg`:
```
[Thu Aug 2 00:00:12 2018] Out of memory: Kill process 1407 (java) score 787 or sacrifice child
[Thu Aug 2 00:00:12 2018] Killed process 1407 (java) total-vm:18876328kB, anon-rss:6323836kB, file-rss:0kB, shmem-rss:0kB
```
- I am still assuming that this is the Tomcat process that is dying, so maybe actually we need to reduce its memory instead of increasing it?
- The risk we run there is that we'll start getting OutOfMemory errors from Tomcat
- So basically we need a new test server with more RAM very soon...
- Abenet asked about the workflow statistics in the Atmire CUA module again
- Last year Atmire told me that it's disabled by default but you can enable it with `workflow.stats.enabled = true` in the CUA configuration file
- There was a bug with adding users so they sent a patch, but I didn't merge it because it was [very dirty](https://github.com/ilri/DSpace/pull/319) and I wasn't sure it actually fixed the problem
- I just tried to enable the stats again on DSpace Test now that we're on DSpace 5.8 with updated Atmire modules, but every user I search for shows "No data available"
- As a test I submitted a new item and I was able to see it in the workflow statistics "data" tab, but not in the graph
2018-08-15 11:56:38 +02:00
## 2018-08-15
- Run through Peter's list of author affiliations from earlier this month
- I did some quick sanity checks and small cleanups in Open Refine, checking for spaces, weird accents, and encoding errors
2018-08-16 14:40:38 +02:00
- Finally I did a test run with the [`fix-metadata-value.py`](https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897) script:
2018-08-15 11:56:38 +02:00
```
$ ./fix-metadata-values.py -i 2018-08-15-Correct-1083-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t correct -m 211
$ ./delete-metadata-values.py -i 2018-08-15-Remove-11-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211
```
2018-08-16 14:40:38 +02:00
## 2018-08-16
- Generate a list of the top 1,500 authors on CGSpace for Sisay so he can create the controlled vocabulary:
```
dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc limit 1500) to /tmp/2018-08-16-top-1500-authors.csv with csv;
```
- Start working on adding the ORCID metadata to a handful of CIAT authors as requested by Elizabeth earlier this month
- I might need to overhaul the [add-orcid-identifiers-csv.py](https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050) script to be a little more robust about author order and ORCID metadata that might have been altered manually by editors after submission, as this script was written without that consideration
2018-08-01 11:49:05 +02:00
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