cgspace-notes/content/post/2016-08.md

+++
date = "2016-08-01T15:53:00+03:00"
author = "Alan Orth"
title = "August, 2016"
tags = ["Notes"]

+++
## 2016-08-01

- Add updated distribution license from Sisay ([#259](https://github.com/ilri/DSpace/issues/259))
- Play with upgrading Mirage 2 dependencies in `bower.json` because most are several versions of out date
- Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more
- bower stuff is a dead end, waste of time, too many issues
- Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of `fonts`)
- Start working on DSpace 5.1 → 5.5 port:

```
$ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
```
<!--more-->

- Lots of conflicts that don't make sense (ie, shouldn't conflict!)
- This file in particular conflicts almost 10 times: `dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss`
- Checking out a clean branch at 5.5 and cherry-picking our commits works where that file would normally have a conflict
- Seems to be related to merge commits
- `git rebase --preserve-merges` doesn't seem to help
- Eventually I just turned on git rerere and solved the conflicts and completed the 403 commit rebase
- The 5.5 code now builds but doesn't run (white page in Tomcat)

## 2016-08-02

- Ask Atmire for help with DSpace 5.5 issue
- Vanilla DSpace 5.5 deploys and runs fine
- Playing with DSpace in Ubuntu 16.04 and Tomcat 7
- Everything is still fucked up, even vanilla DSpace 5.5

## 2016-08-04

- Ask on DSpace mailing list about duplicate authors, Discovery and author text values
- Atmire responded with some new DSpace 5.5 ready versions to try for their modules

## 2016-08-05

- Fix item display incorrectly displaying Species when Breeds were present ([#260](https://github.com/ilri/DSpace/pull/260))
- Experiment with fixing more authors, like Delia Grace:

```
dspacetest=# update metadatavalue set authority='0b4fcbc1-d930-4319-9b4d-ea1553cca70b', confidence=600 where metadata_field_id=3 and text_value='Grace, D.';
```

## 2016-08-06

- Finally figured out how to remove "View/Open" and "Bitstreams" from the item view

## 2016-08-07

- Start working on Ubuntu 16.04 Ansible playbook for Tomcat 8, PostgreSQL 9.5, Oracle 8, etc

## 2016-08-08

- Still troubleshooting Atmire modules on DSpace 5.5
- Vanilla DSpace 5.5 works on Tomcat 7...
- Ooh, and vanilla DSpace 5.5 works on Tomcat 8 with Java 8!
- Some notes about setting up Tomcat 8, since it's new on this machine...
- Install latest Oracle Java 8 JDK
- Create `setenv.sh` in Tomcat 8 `libexec/bin` directory:

```
CATALINA_OPTS="-Djava.awt.headless=true -Xms3072m -Xmx3072m -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -Dfile.encoding=UTF-8"
CATALINA_OPTS="$CATALINA_OPTS -Djava.library.path=/opt/brew/Cellar/tomcat-native/1.2.8/lib"

JRE_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home
```

- Edit Tomcat 8 `server.xml` to add regular HTTP listener for solr
- Symlink webapps:

```
$ rm -rf /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
$ ln -sv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
$ ln -sv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/oai
$ ln -sv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/jspui
$ ln -sv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/rest
$ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/solr
```

## 2016-08-09

- More tests of Atmire's 5.5 modules on a clean, working instance of `5_x-prod`
- Still fails, though perhaps differently than before (Flyway): https://gist.github.com/alanorth/5d49c45a16efd7c6bc1e6642e66118b2
- More work on Tomcat 8 and Java 8 stuff for Ansible playbooks

## 2016-08-10

- Turns out DSpace 5.x isn't ready for Tomcat 8: https://jira.duraspace.org/browse/DS-3092
- So we'll need to use Tomcat 7 + Java 8 on Ubuntu 16.04
- More work on the Ansible stuff for this, allowing Tomcat 7 to use Java 8
- Merge pull request for fixing the type Discovery index to use `dc.type` ([#262](https://github.com/ilri/DSpace/pull/262))
- Merge pull request for removing "Bitstream" text from item display, as it confuses users and isn't necessary ([#263](https://github.com/ilri/DSpace/pull/263))

## 2016-08-11

- Finally got DSpace (5.5) running on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5 via the updated Ansible stuff

![DSpace 5.5 on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5](2016/08/dspace55-ubuntu16.04.png)

## 2016-08-14

- Update Mirage 2 build notes for Ubuntu 16.04: https://gist.github.com/alanorth/2cf9c15834dc68a514262fcb04004cb0

## 2016-08-15

- Notes on NodeJS + nginx + systemd: https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1

![ExpressJS running behind nginx](2016/08/nodejs-nginx.png)

## 2016-08-16

- Troubleshoot Paramiko connection issues with Ansible on ILRI servers: [#37](https://github.com/ilri/rmg-ansible-public/issues/37)
- Turns out we need to add some MACs to our `sshd_config`: hmac-sha2-512,hmac-sha2-256
- Update DSpace Test's Java to version 8 to start testing this configuration ([seeing as Solr recommends it](https://wiki.apache.org/solr/ShawnHeisey))

## 2016-08-17

- More work on Let's Encrypt stuff for Ansible roles
- Yesterday Atmire responded about DSpace 5.5 issues and asked me to try the `dspace database repair` command to fix Flyway issues
- The `dspace database` command doesn't even run: https://gist.github.com/alanorth/c43c8d89e8df346d32c0ee938be90cd5
- Oops, it looks like the missing classes causing `dspace database` to fail were coming from the old `~/dspace/config/spring` folder
- After removing the spring folder and running ant install again, `dspace database` works
- I see there are missing and pending Flyway migrations, but running `dspace database repair` and `dspace database migrate` does nothing: https://gist.github.com/alanorth/41ed5abf2ff32d8ac9eedd1c3d015d70

## 2016-08-18

- Fix "CONGO,DR" country name in `input-forms.xml` ([#264](https://github.com/ilri/DSpace/pull/264))
- Also need to fix existing records using the incorrect form in the database:

```
dspace=# update metadatavalue set text_value='CONGO, DR' where resource_type_id=2 and metadata_field_id=228 and text_value='CONGO,DR';
```

- I asked a question on the DSpace mailing list about updating "preferred" forms of author names from ORCID

## 2016-08-21

- A few days ago someone on the DSpace mailing list suggested I try `dspace dsrun org.dspace.authority.UpdateAuthorities` to update preferred author names from ORCID
- If you set `auto-update-items=true` in `dspace/config/modules/solrauthority.cfg` it is supposed to update records it finds automatically
- I updated my name format on ORCID and I've been running that script a few times per day since then but nothing has changed
- Still troubleshooting Atmire modules on DSpace 5.5
- I sent them some new verbose logs: https://gist.github.com/alanorth/700748995649688148ceba89d760253e

## 2016-08-22

- Database migrations are fine on DSpace 5.1:

```
$ ~/dspace/bin/dspace database info

Database URL: jdbc:postgresql://localhost:5432/dspacetest
Database Schema: public
Database Software: PostgreSQL version 9.3.14
Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 901)

+----------------+----------------------------+---------------------+---------+
| Version        | Description                | Installed on        | State   |
+----------------+----------------------------+---------------------+---------+
| 1.1            | Initial DSpace 1.1 databas |                     | PreInit |
| 1.2            | Upgrade to DSpace 1.2 sche |                     | PreInit |
| 1.3            | Upgrade to DSpace 1.3 sche |                     | PreInit |
| 1.3.9          | Drop constraint for DSpace |                     | PreInit |
| 1.4            | Upgrade to DSpace 1.4 sche |                     | PreInit |
| 1.5            | Upgrade to DSpace 1.5 sche |                     | PreInit |
| 1.5.9          | Drop constraint for DSpace |                     | PreInit |
| 1.6            | Upgrade to DSpace 1.6 sche |                     | PreInit |
| 1.7            | Upgrade to DSpace 1.7 sche |                     | PreInit |
| 1.8            | Upgrade to DSpace 1.8 sche |                     | PreInit |
| 3.0            | Upgrade to DSpace 3.x sche |                     | PreInit |
| 4.0            | Initializing from DSpace 4 | 2015-11-20 12:42:52 | Success |
| 5.0.2014.08.08 | DS-1945 Helpdesk Request a | 2015-11-20 12:42:53 | Success |
| 5.0.2014.09.25 | DS 1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
| 5.0.2014.09.26 | DS-1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
| 5.0.2015.01.27 | MigrateAtmireExtraMetadata | 2015-11-20 12:43:29 | Success |
| 5.1.2015.12.03 | Atmire CUA 4 migration     | 2016-03-21 17:10:41 | Success |
| 5.1.2015.12.03 | Atmire MQM migration       | 2016-03-21 17:10:42 | Success |
+----------------+----------------------------+---------------------+---------+
```

- So I'm not sure why they have problems when we move to DSpace 5.5 (even the 5.1 migrations themselves show as "Missing")

## 2016-08-23

- Help Paola from CCAFS with her thumbnails again
- Talk to Atmire about the DSpace 5.5 issue, and it seems to be caused by a bug in FlywayDB
- They said I should delete the Atmire migrations

```
dspacetest=# delete from schema_version where description =  'Atmire CUA 4 migration' and version='5.1.2015.12.03.2';
dspacetest=# delete from schema_version where description =  'Atmire MQM migration' and version='5.1.2015.12.03.3';
```

- After that DSpace starts up by XMLUI now has unrelated issues that I need to solve!

```
org.apache.avalon.framework.configuration.ConfigurationException: Type 'ThemeResourceReader' does not exist for 'map:read' at jndi:/localhost/themes/0_CGIAR/sitemap.xmap:136:77
context:/jndi:/localhost/themes/0_CGIAR/sitemap.xmap - 136:77
```

- Looks like we're missing some stuff in the XMLUI module's `sitemap.xmap`, as well as in each of our XMLUI themes
- Diff them with these to get the `ThemeResourceReader` changes:
  - `dspace-xmlui/src/main/webapp/sitemap.xmap`
  - `dspace-xmlui-mirage2/src/main/webapp/sitemap.xmap`
- Then we had some NullPointerException from the SolrLogger class, which is apparently part of Atmire's CUA module
- I tried with a small version bump to CUA but it didn't work (version `5.5-4.1.1-0`)
- Also, I started looking into huge pages to prepare for PostgreSQL 9.5, but it seems Linode's kernels don't enable them

## 2016-08-24

- Clean up and import 48 CCAFS records into DSpace Test
- SQL to get all journal titles from dc.source (55), since it's apparently used for internal DSpace filename shit, but we moved all our journal titles there a few months ago:

```
dspacetest=# select distinct text_value from metadatavalue where metadata_field_id=55 and text_value !~ '.*(\.pdf|\.png|\.PDF|\.Pdf|\.JPEG|\.jpg|\.JPG|\.jpeg|\.xls|\.rtf|\.docx?|\.potx|\.dotx|\.eqa|\.tiff|\.mp4|\.mp3|\.gif|\.zip|\.txt|\.pptx|\.indd|\.PNG|\.bmp|\.exe|org\.dspace\.app\.mediafilter).*';
```

## 2016-08-25

- Atmire suggested adding a missing bean to `dspace/config/spring/api/atmire-cua.xml` but it doesn't help:

```
...
Error creating bean with name 'MetadataStorageInfoService'
...
```

- Atmire sent an updated version of `dspace/config/spring/api/atmire-cua.xml` and now XMLUI starts but gives a null pointer exception:

```
Java stacktrace: java.lang.NullPointerException
    at org.dspace.app.xmlui.aspect.statistics.Navigation.addOptions(Navigation.java:129)
    at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:228)
    at sun.reflect.GeneratedMethodAccessor126.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
    at com.sun.proxy.$Proxy103.startElement(Unknown Source)
    at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
    at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
    at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
...
```

- Import the 47 CCAFS records to CGSpace, creating the SimpleArchiveFormat bundles and importing like:

```
$ ./safbuilder.sh -c /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/3546.csv
$ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgiar.org/bin/dspace import -a -e aorth@mjanja.ch -c 10568/3546 -s /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/SimpleArchiveFormat -m 3546.map
```

- Finally got DSpace 5.5 working with the Atmire modules after a few rounds of back and forth with Atmire devs

## 2016-08-26

- CGSpace had issues tonight, not entirely crashing, but becoming unresponsive
- The dspace log had this:

```
2016-08-26 20:48:05,040 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
```

- Related to /rest no doubt

## 2016-08-27

- Run corrections for Delia Grace and `CONGO, DR`, and deploy August changes to CGSpace
- Run all system updates and reboot the server