cgspace-notes/content/posts/2018-07.md

---
title: "July, 2018"
date: 2018-07-01T12:56:54+03:00
author: "Alan Orth"
tags: ["Notes"]
---

## 2018-07-01

- I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:

```
$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
```

- During the `mvn package` stage on the 5.8 branch I kept getting issues with java running out of memory:

```
There is insufficient memory for the Java Runtime Environment to continue.
```

<!--more-->

- As the machine only has 8GB of RAM, I reduced the Tomcat memory heap from 5120m to 4096m so I could try to allocate more to the build process:

```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
$ mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -Denv=dspacetest.cgiar.org -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2 clean package
```

- Then I stopped the Tomcat 7 service, ran the ant update, and manually ran the old and ignored SQL migrations:

```
$ sudo su - postgres
$ psql dspace
...
dspace=# begin;
BEGIN
dspace=# \i Atmire-DSpace-5.8-Schema-Migration.sql
DELETE 0
UPDATE 1
DELETE 1
dspace=# commit
dspace=# \q
$ exit
$ dspace database migrate ignored
```

- After that I started Tomcat 7 and DSpace seems to be working, now I need to tell our colleagues to try stuff and report issues they have

## 2018-07-02

- Discuss AgriKnowledge including our Handle identifier on their harvested items from CGSpace
- They seem to be only interested in Gates-funded outputs, for example: https://www.agriknowledge.org/files/tm70mv21t

## 2018-07-03

- Finally finish with the CIFOR Archive records (a total of 2448):
  - I mapped the 50 items that were duplicates from elsewhere in CGSpace into [CIFOR Archive](https://cgspace.cgiar.org/handle/10568/16702)
  - I did one last check of the remaining 2398 items and found eight who have a `cg.identifier.doi` that links to some URL other than a DOI so I moved those to `cg.identifier.url` and `cg.identifier.googleurl` as appropriate
  - Also, thirteen items had a DOI in their citation, but did not have a `cg.identifier.doi` field, so I added those
  - Then I imported those 2398 items in two batches (to deal with memory issues):

```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive.csv
$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive2.csv
```

- I noticed there are many items that use HTTP instead of HTTPS for their Google Books URL, and some missing HTTP entirely:

```
dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
 count
-------
   785
dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
 count
-------
     4
```

- I think I should fix that as well as some other garbage values like "test" and "dspace.ilri.org" etc:

```
dspace=# begin;
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
UPDATE 785
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
UPDATE 4
dspace=# update metadatavalue set text_value='https://books.google.com/books?id=meF1CLdPSF4C' where resource_type_id=2 and metadata_field_id=222 and text_value='meF1CLdPSF4C';
UPDATE 1
dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=222 and metadata_value_id in (2299312, 10684, 10700, 996403);
DELETE 4
dspace=# commit;
```

- Testing DSpace 5.8 with PostgreSQL 9.6 and Tomcat 8.5.32 (instead of my usual 7.0.88) and for some reason I get autowire errors on Catalina startup with 8.5.32:

```
03-Jul-2018 19:51:37.272 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener]
 java.lang.RuntimeException: Failure during filter init: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
	at org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener.contextInitialized(DSpaceKernelServletContextListener.java:92)
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
	at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:629)
	at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1839)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
```

- Gotta check that out later...

## 2018-07-04

- I verified that the autowire error indeed only occurs on Tomcat 8.5, but the application works fine on Tomcat 7
- I have raised this in the [DSpace 5.8 compatibility ticket on Atmire's tracker](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560)
- Abenet wants me to add "United Kingdom government" to the sponsors on CGSpace so I created a ticket to track it ([#381](https://github.com/ilri/DSpace/issues/381))
- Also, Udana wants me to add "Enhancing Sustainability Across Agricultural Systems" to the WLE Phase II research themes so I created a ticket to track that ([#382](https://github.com/ilri/DSpace/issues/382)
- I need to try to finish this DSpace 5.8 business first because I have too many branches with cherry-picks going on right now!

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