cgspace-notes/content/posts/2016-05.md

+++
date = "2016-05-01T23:06:00+03:00"
author = "Alan Orth"
title = "May, 2016"
tags = ["Notes"]

+++
## 2016-05-01

- Since yesterday there have been 10,000 REST errors and the site has been unstable again
- I have blocked access to the API now
- There are 3,000 IPs accessing the REST API in a 24-hour period!

```
# awk '{print $1}' /var/log/nginx/rest.log  | uniq | wc -l
3168
```

<!--more-->

- The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29
- 100% of the requests coming from Ethiopia are like this and result in an HTTP 500:

```
GET /rest/handle/10568/NaN?expand=parentCommunityList,metadata HTTP/1.1
```

- For now I'll block just the Ethiopian IP
- The owner of that application has said that the `NaN` (not a number) is an error in his code and he'll fix it

## 2016-05-03

- Update nginx to 1.10.x branch on CGSpace
- Fix a reference to `dc.type.output` in Discovery that I had missed when we migrated to `dc.type` last month ([#223](https://github.com/ilri/DSpace/pull/223))

![Item type in Discovery results](/cgspace-notes/2016/05/discovery-types.png)

## 2016-05-06

- DSpace Test is down, `catalina.out` has lots of messages about heap space from some time yesterday (!)
- It looks like Sisay was doing some batch imports
- Hmm, also disk space is full
- I decided to blow away the solr indexes, since they are 50GB and we don't really need all the Atmire stuff there right now
- I will re-generate the Discovery indexes after re-deploying
- Testing `renew-letsencrypt.sh` script for nginx

```
#!/usr/bin/env bash

readonly SERVICE_BIN=/usr/sbin/service
readonly LETSENCRYPT_BIN=/opt/letsencrypt/letsencrypt-auto

# stop nginx so LE can listen on port 443
$SERVICE_BIN nginx stop

$LETSENCRYPT_BIN renew -nvv --standalone --standalone-supported-challenges tls-sni-01 > /var/log/letsencrypt/renew.log 2>&1

LE_RESULT=$?

$SERVICE_BIN nginx start

if [[ "$LE_RESULT" != 0 ]]; then
    echo 'Automated renewal failed:'

    cat /var/log/letsencrypt/renew.log

    exit 1
fi
```

- Seems to work well

## 2016-05-10

- Start looking at more metadata migrations
- There are lots of fields in `dcterms` namespace that look interesting, like:
  - dcterms.type
  - dcterms.spatial
- Not sure what `dcterms` is...
- Looks like these were [added in DSpace 4](https://wiki.lyrasis.org/display/DSDOC5x/Metadata+and+Bitstream+Format+Registries#MetadataandBitstreamFormatRegistries-DublinCoreTermsRegistry(DCTERMS)) to allow for future work to make DSpace more flexible
- CGSpace's `dc` registry has 96 items, and the default DSpace one has 73.

## 2016-05-11

- Identify and propose the next phase of CGSpace fields to migrate:
  - dc.title.jtitle      → cg.title.journal
  - dc.identifier.status → cg.identifier.status
  - dc.river.basin       → cg.river.basin
  - dc.Species           → cg.species
  - dc.targetaudience    → cg.targetaudience
  - dc.fulltextstatus    → cg.fulltextstatus
  - dc.editon            → cg.edition
  - dc.isijournal        → cg.isijournal

- Start a test rebase of the `5_x-prod` branch on top of the `dspace-5.5` tag
- There were a handful of conflicts that I didn't understand
- After completing the rebase I tried to build with the module versions Atmire had indicated as being 5.5 ready but I got this error:

```
[ERROR] Failed to execute goal on project additions: Could not resolve dependencies for project org.dspace.modules:additions:jar:5.5: Could not find artifact com.atmire:atmire-metadata-quality-api:jar:5.5-2.10.1-0 in sonatype-releases (https://oss.sonatype.org/content/repositories/releases/) -> [Help 1]
```

- I've sent them a question about it
- A user mentioned having problems with uploading a 33 MB PDF
- I told her I would increase the limit temporarily tomorrow morning
- Turns out she was able to decrease the size of the PDF so we didn't have to do anything

## 2016-05-12

- Looks like the issue that Abenet was having a few days ago with "Connection Reset" in Firefox might be due to a Firefox 46 issue: https://bugzilla.mozilla.org/show_bug.cgi?id=1268775
- I finally found a copy of the latest CG Core metadata guidelines and it looks like we can add a few more fields to our next migration:
  - dc.rplace.region  → cg.coverage.region
  - dc.cplace.country → cg.coverage.country
- Questions for CG people:
  - Our `dc.place` and `dc.srplace.subregion` could both map to `cg.coverage.admin-unit`?
  - Should we use `dc.contributor.crp` or `cg.contributor.crp` for the CRP (ours is `dc.crsubject.crpsubject`)?
  - Our `dc.contributor.affiliation` and `dc.contributor.corporate` could both map to `dc.contributor` and possibly `dc.contributor.center` depending on if it's a CG center or not
  - `dc.title.jtitle` could either map to `dc.publisher` or `dc.source` depending on how you read things
- Found ~200 messed up CIAT values in `dc.publisher`:

```
# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to "%  %";
```

## 2016-05-13

- More theorizing about CGcore
- Add two new fields:
  - dc.srplace.subregion → cg.coverage.admin-unit
  - dc.place → cg.place
- `dc.place` is our own field, so it's easy to move
- I've removed `dc.title.jtitle` from the list for now because there's no use moving it out of DC until we know where it will go (see discussion yesterday)

## 2016-05-18

- Work on 707 CCAFS records
- They have thumbnails on Flickr and elsewhere
- In OpenRefine I created a new `filename` column based on the `thumbnail` column with the following GREL:

```
if(cells['thumbnails'].value.contains('hqdefault'), cells['thumbnails'].value.split('/')[-2] + '.jpg', cells['thumbnails'].value.split('/')[-1])
```

- Because ~400 records had the same filename on Flickr (hqdefault.jpg) but different UUIDs in the URL
- So for the `hqdefault.jpg` ones I just take the UUID (-2) and use it as the filename
- Before importing with SAFBuilder I tested adding "__bundle:THUMBNAIL" to the `filename` column and it works fine

## 2016-05-19

- More quality control on `filename` field of CCAFS records to make processing in shell and SAFBuilder more reliable:

```
value.replace('_','').replace('-','')
```

- We need to hold off on moving `dc.Species` to `cg.species` because it is only used for plants, and might be better to move it to something like `cg.species.plant`
- And `dc.identifier.fund` is MOSTLY used for CPWF project identifier but has some other sponsorship things
  - We should move PN*, SG*, CBA, IA, and PHASE* values to `cg.identifier.cpwfproject`
  - The rest, like BMGF and USAID etc, might have to go to either `dc.description.sponsorship` or `cg.identifier.fund` (not sure yet)
  - There are also some mistakes in CPWF's things, like "PN 47"
  - This ought to catch all the CPWF values (there don't appear to be and SG* values):

```
# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
```

## 2016-05-20

- More work on CCAFS Video and Images records
- For SAFBuilder we need to modify filename column to have the thumbnail bundle:
    
```
value + "__bundle:THUMBNAIL"
```

- Also, I fixed some weird characters using OpenRefine's transform with the following GREL:

```
value.replace(/\u0081/,'')
```

- Write shell script to resize thumbnails with height larger than 400: https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256
- Upload 707 CCAFS records to DSpace Test
- A few miscellaneous fixes for XMLUI display niggles (spaces in item lists and link target `_black`): [#224](https://github.com/ilri/DSpace/pull/224)
- Work on configuration changes for Phase 2 metadata migrations

## 2016-05-23

- Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine
- LibreOffice excludes empty cells when it exports and all the fields shift over to the left and cause URLs to go to Subjects, etc.
- Google Docs does this better, but somehow reorders the rows and when I paste the thumbnail/filename row in they don't match!
- I will have to try later

## 2016-05-30

- Export CCAFS video and image records from DSpace Test using the migrate option (`-m`):

```
$ mkdir ~/ccafs-images
$ /home/dspacetest.cgiar.org/bin/dspace export -t COLLECTION -i 10568/79355 -d ~/ccafs-images -n 0 -m
```

- And then import to CGSpace:

```
$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/70974 --source /tmp/ccafs-images --mapfile=/tmp/ccafs-images-may30.map &> /tmp/ccafs-images-may30.log
```

- But now we have double authors for "CGIAR Research Program on Climate Change, Agriculture and Food Security" in the authority
- I'm trying to do a Discovery index before messing with the authority index
- Looks like we are missing the `index-authority` cron job, so who knows what's up with our authority index
- Run system updates on DSpace Test, re-deploy code, and reboot the server
- Clean up and import ~200 CTA records to CGSpace via CSV like:

```
$ export JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8"
$ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA-May30/CTA-42229.csv &> ~/CTA-May30/CTA-42229.log
```

- Discovery indexing took a few hours for some reason, and after that I started the `index-authority` script

```
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace index-authority
```

## 2016-05-31

- The `index-authority` script ran over night and was finished in the morning
- Hopefully this was because we haven't been running it regularly and it will speed up next time
- I am running it again with a timer to see:

```
$ time /home/cgspace.cgiar.org/bin/dspace index-authority
Retrieving all data
Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
Cleaning the old index
Writing new data
All done !

real    37m26.538s
user    2m24.627s
sys     0m20.540s
```

- Update `tomcat7` crontab on CGSpace and DSpace Test to have the `index-authority` script that we were missing
- Add new ILRI subject and CCAFS project tags to `input-forms.xml` ([#226](https://github.com/ilri/DSpace/pull/226), [#225](https://github.com/ilri/DSpace/pull/225))
- Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.
- Re-sync DSpace Test data with CGSpace
- Clean up and import ~65 more CTA items into CGSpace