cgspace-notes/content/post/2016-07.md

+++
date = "2016-07-01T10:53:00+03:00"
author = "Alan Orth"
title = "July, 2016"
tags = ["Notes"]

+++
## 2016-07-01

- Add `dc.description.sponsorship` to Discovery sidebar facets and make investors clickable in item view ([#232](https://github.com/ilri/DSpace/issues/232))
- I think this query should find and replace all authors that have "," at the end of their names:

```
dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
UPDATE 95
dspacetest=# select text_value from  metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
 text_value
------------
(0 rows)
```

- In this case the select query was showing 95 results before the update

<!--more-->

## 2016-07-02

- Comment on DSpace Jira ticket about author lookup search text ([DS-2329](https://jira.duraspace.org/browse/DS-2329))

## 2016-07-04

- Seems the database's author authority values mean nothing without the `authority` Solr core from the host where they were created!

## 2016-07-05

- Amend `backup-solr.sh` script so it backs up the entire Solr folder
- We *really* only need `statistics` and `authority` but meh
- Fix metadata for species on DSpace Test:

```
$ ./fix-metadata-values.py -i /tmp/Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 94 -d dspacetest -u dspacetest -p 'fuuu'
```

- Will run later on CGSpace
- A user is still having problems with Sherpa/Romeo causing crashes during the submission process when the journal is "ungraded"
- I tested the [patch for DS-2740](https://jira.duraspace.org/browse/DS-2740) that I had found last month and it seems to work
- I will merge it to `5_x-prod`

## 2016-07-06

- Delete 23 blank metadata values from CGSpace:

```
cgspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
DELETE 23
```

- Complete phase three of metadata migration, for the following fields:
  - dc.title.jtitle → dc.source
  - dc.crsubject.crpsubject → cg.contributor.crp
  - dc.contributor.affiliation → cg.contributor.affiliation
  - dc.Species → cg.species
  - dc.srplace.subregion → cg.coverage.subregion
  - dc.contributor.corporate → dc.contributor.author
  - dc.identifier.url → cg.identifier.url
  - dc.identifier.doi → cg.identifier.doi
  - dc.identifier.googleurl → cg.identifier.googleurl
  - dc.identifier.dataurl → cg.identifier.dataurl
- Also, run fixes and deletes for species and author affiliations (over 1000 corrections!)

```
$ ./fix-metadata-values.py -i Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 212 -d dspace -u dspace -p 'fuuu'
$ ./fix-metadata-values.py -i Affiliations-Fix-1045-Peter-Abenet.csv -f dc.contributor.affiliation -t Correct -m 211 -d dspace -u dspace -p 'fuuu'
$ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Delete-Peter-Abenet.csv -m 211 -u dspace -d dspace -p 'fuuu'
```

- I then ran all server updates and rebooted the server

## 2016-07-11

- Doing some author cleanups from Peter and Abenet:

```
$ ./fix-metadata-values.py -i /tmp/Authors-Fix-205-UTF8.csv -f dc.contributor.author -t correct -m 3 -d dspacetest -u dspacetest -p fuuu
$ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu
```

## 2016-07-13

- Run the author cleanups on CGSpace and start a full Discovery re-index

## 2016-07-14

- Test LDAP settings for new root LDAP
- Seems to work when binding as a top-level user

## 2016-07-18

- Adjust identifiers in XMLUI item display to be more prominent
- Add species and breed to the XMLUI item display
- CGSpace crashed late at night and the DSpace logs were showing:

```
2016-07-18 20:26:30,941 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
...
```

- I suspect it's someone hitting REST too much:

```
# awk '{print $1}' /var/log/nginx/rest.log  | sort -n | uniq -c | sort -h | tail -n 3
    710 66.249.78.38
   1781 181.118.144.29
  24904 70.32.99.142
```

- I just blocked access to `/rest` for that last IP for now:

```
     # log rest requests
     location /rest {
         access_log /var/log/nginx/rest.log;
         proxy_pass http://127.0.0.1:8443;
         deny 70.32.99.142;
     }
```

## 2016-07-21

- Mitigate the [HTTPoxy](https://httpoxy.org) vulnerability for Tomcat etc in nginx: https://github.com/ilri/rmg-ansible-public/pull/38
- Unblock 70.32.99.142 from `/rest` as it has been blocked for a few days

## 2016-07-22

- Help Paola from CCAFS with thumbnails for batch uploads
- She has been struggling to get the dimensions right, and manually enlarging smaller thumbnails, renaming PNGs to JPG, etc
- Altmetric reports having an issue with some of our authors being doubled...
- This is related to authority and confidence!
- We might need to use `index.authority.ignore-prefered=true` to tell the Discovery index to prefer the variation that exists in the metadatavalue rather than what it finds in the authority cache.
- Trying these on DSpace Test after a discussion by Daniel Scharon on the dspace-tech mailing list:

```
index.authority.ignore-prefered.dc.contributor.author=true
index.authority.ignore-variants.dc.contributor.author=false
```

- After reindexing I don't see any change in Discovery's display of authors, and still have entries like:

```
Grace, D. (464)
Grace, D. (62)
```

- I asked for clarification of the following options on the DSpace mailing list:

```
index.authority.ignore
index.authority.ignore-prefered
index.authority.ignore-variants
```

- In the mean time, I will try these on DSpace Test (plus a reindex):

```
index.authority.ignore=true
index.authority.ignore-prefered=true
index.authority.ignore-variants=true
```

- Enabled usage of `X-Forwarded-For` in DSpace admin control panel ([#255](https://github.com/ilri/DSpace/pull/255)
- It was misconfigured and disabled, but already working for some reason *sigh*
- ... no luck. Trying with just:

```
index.authority.ignore=true
```

- After re-indexing and clearing the XMLUI cache nothing has changed

## 2016-07-25

- Trying a few more settings (plus reindex) for Discovery on DSpace Test:

```
index.authority.ignore-prefered.dc.contributor.author=true
index.authority.ignore-variants=true
```

- Run all OS updates and reboot DSpace Test server
- No changes to Discovery after reindexing... hmm.
- Integrate and massively clean up About page ([#256](https://github.com/ilri/DSpace/pull/256))

![About page](2016/07/cgspace-about-page.png)

- The DSpace source code mentions the configuration key `discovery.index.authority.ignore-prefered.*` (with prefix of discovery, despite the docs saying otherwise), so I'm trying the following on DSpace Test:

```
discovery.index.authority.ignore-prefered.dc.contributor.author=true
discovery.index.authority.ignore-variants=true
```

- Still no change!
- Deploy species, breed, and identifier changes to CGSpace, as well as About page
- Run Linode RAM upgrade (8→12GB)
- Re-sync DSpace Test with CGSpace
- I noticed that our backup scripts don't send Solr cores to S3 so I amended the script

## 2016-07-31

- Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by
- Also change "Subjects" to "AGROVOC keywords" in Discovery sidebar/search and Browse by ([#257](https://github.com/ilri/DSpace/issues/257))