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Alan Orth
d3d413c991
The theme used to have a <base> tag, which tells the browser which base to use for relative URLs, but this was actually a buggy and incorrect theme behavior, so we need to update our links. $ sed -i 's/(\(201[567]\)/(\/cgspace-notes\/\1/' content/post/*.md
277 lines
13 KiB
Markdown
277 lines
13 KiB
Markdown
+++
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date = "2016-08-01T15:53:00+03:00"
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author = "Alan Orth"
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title = "August, 2016"
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tags = ["Notes"]
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+++
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## 2016-08-01
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- Add updated distribution license from Sisay ([#259](https://github.com/ilri/DSpace/issues/259))
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- Play with upgrading Mirage 2 dependencies in `bower.json` because most are several versions of out date
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- 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
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- bower stuff is a dead end, waste of time, too many issues
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- Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of `fonts`)
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- Start working on DSpace 5.1 → 5.5 port:
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```
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$ git checkout -b 55new 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.5
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```
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<!--more-->
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- Lots of conflicts that don't make sense (ie, shouldn't conflict!)
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- This file in particular conflicts almost 10 times: `dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss`
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- Checking out a clean branch at 5.5 and cherry-picking our commits works where that file would normally have a conflict
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- Seems to be related to merge commits
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- `git rebase --preserve-merges` doesn't seem to help
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- Eventually I just turned on git rerere and solved the conflicts and completed the 403 commit rebase
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- The 5.5 code now builds but doesn't run (white page in Tomcat)
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## 2016-08-02
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- Ask Atmire for help with DSpace 5.5 issue
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- Vanilla DSpace 5.5 deploys and runs fine
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- Playing with DSpace in Ubuntu 16.04 and Tomcat 7
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- Everything is still fucked up, even vanilla DSpace 5.5
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## 2016-08-04
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- Ask on DSpace mailing list about duplicate authors, Discovery and author text values
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- Atmire responded with some new DSpace 5.5 ready versions to try for their modules
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## 2016-08-05
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- Fix item display incorrectly displaying Species when Breeds were present ([#260](https://github.com/ilri/DSpace/pull/260))
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- Experiment with fixing more authors, like Delia Grace:
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```
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dspacetest=# update metadatavalue set authority='0b4fcbc1-d930-4319-9b4d-ea1553cca70b', confidence=600 where metadata_field_id=3 and text_value='Grace, D.';
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```
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## 2016-08-06
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- Finally figured out how to remove "View/Open" and "Bitstreams" from the item view
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## 2016-08-07
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- Start working on Ubuntu 16.04 Ansible playbook for Tomcat 8, PostgreSQL 9.5, Oracle 8, etc
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## 2016-08-08
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- Still troubleshooting Atmire modules on DSpace 5.5
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- Vanilla DSpace 5.5 works on Tomcat 7...
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- Ooh, and vanilla DSpace 5.5 works on Tomcat 8 with Java 8!
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- Some notes about setting up Tomcat 8, since it's new on this machine...
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- Install latest Oracle Java 8 JDK
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- Create `setenv.sh` in Tomcat 8 `libexec/bin` directory:
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```
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CATALINA_OPTS="-Djava.awt.headless=true -Xms3072m -Xmx3072m -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -Dfile.encoding=UTF-8"
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CATALINA_OPTS="$CATALINA_OPTS -Djava.library.path=/opt/brew/Cellar/tomcat-native/1.2.8/lib"
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JRE_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home
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```
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- Edit Tomcat 8 `server.xml` to add regular HTTP listener for solr
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- Symlink webapps:
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```
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$ rm -rf /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
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$ ln -sv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
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$ ln -sv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/oai
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$ ln -sv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/jspui
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$ ln -sv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/rest
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$ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/solr
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```
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## 2016-08-09
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- More tests of Atmire's 5.5 modules on a clean, working instance of `5_x-prod`
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- Still fails, though perhaps differently than before (Flyway): https://gist.github.com/alanorth/5d49c45a16efd7c6bc1e6642e66118b2
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- More work on Tomcat 8 and Java 8 stuff for Ansible playbooks
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## 2016-08-10
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- Turns out DSpace 5.x isn't ready for Tomcat 8: https://jira.duraspace.org/browse/DS-3092
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- So we'll need to use Tomcat 7 + Java 8 on Ubuntu 16.04
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- More work on the Ansible stuff for this, allowing Tomcat 7 to use Java 8
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- Merge pull request for fixing the type Discovery index to use `dc.type` ([#262](https://github.com/ilri/DSpace/pull/262))
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- 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))
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## 2016-08-11
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- Finally got DSpace (5.5) running on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5 via the updated Ansible stuff
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## 2016-08-14
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- Update Mirage 2 build notes for Ubuntu 16.04: https://gist.github.com/alanorth/2cf9c15834dc68a514262fcb04004cb0
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## 2016-08-15
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- Notes on NodeJS + nginx + systemd: https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1
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## 2016-08-16
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- Troubleshoot Paramiko connection issues with Ansible on ILRI servers: [#37](https://github.com/ilri/rmg-ansible-public/issues/37)
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- Turns out we need to add some MACs to our `sshd_config`: hmac-sha2-512,hmac-sha2-256
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- Update DSpace Test's Java to version 8 to start testing this configuration ([seeing as Solr recommends it](https://wiki.apache.org/solr/ShawnHeisey))
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## 2016-08-17
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- More work on Let's Encrypt stuff for Ansible roles
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- Yesterday Atmire responded about DSpace 5.5 issues and asked me to try the `dspace database repair` command to fix Flyway issues
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- The `dspace database` command doesn't even run: https://gist.github.com/alanorth/c43c8d89e8df346d32c0ee938be90cd5
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- Oops, it looks like the missing classes causing `dspace database` to fail were coming from the old `~/dspace/config/spring` folder
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- After removing the spring folder and running ant install again, `dspace database` works
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- 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
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## 2016-08-18
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- Fix "CONGO,DR" country name in `input-forms.xml` ([#264](https://github.com/ilri/DSpace/pull/264))
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- Also need to fix existing records using the incorrect form in the database:
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```
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dspace=# update metadatavalue set text_value='CONGO, DR' where resource_type_id=2 and metadata_field_id=228 and text_value='CONGO,DR';
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```
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- I asked a question on the DSpace mailing list about updating "preferred" forms of author names from ORCID
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## 2016-08-21
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- 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
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- If you set `auto-update-items=true` in `dspace/config/modules/solrauthority.cfg` it is supposed to update records it finds automatically
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- 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
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- Still troubleshooting Atmire modules on DSpace 5.5
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- I sent them some new verbose logs: https://gist.github.com/alanorth/700748995649688148ceba89d760253e
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## 2016-08-22
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- Database migrations are fine on DSpace 5.1:
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```
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$ ~/dspace/bin/dspace database info
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Database URL: jdbc:postgresql://localhost:5432/dspacetest
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Database Schema: public
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Database Software: PostgreSQL version 9.3.14
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Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 901)
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+----------------+----------------------------+---------------------+---------+
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| Version | Description | Installed on | State |
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+----------------+----------------------------+---------------------+---------+
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| 1.1 | Initial DSpace 1.1 databas | | PreInit |
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| 1.2 | Upgrade to DSpace 1.2 sche | | PreInit |
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| 1.3 | Upgrade to DSpace 1.3 sche | | PreInit |
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| 1.3.9 | Drop constraint for DSpace | | PreInit |
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| 1.4 | Upgrade to DSpace 1.4 sche | | PreInit |
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| 1.5 | Upgrade to DSpace 1.5 sche | | PreInit |
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| 1.5.9 | Drop constraint for DSpace | | PreInit |
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| 1.6 | Upgrade to DSpace 1.6 sche | | PreInit |
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| 1.7 | Upgrade to DSpace 1.7 sche | | PreInit |
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| 1.8 | Upgrade to DSpace 1.8 sche | | PreInit |
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| 3.0 | Upgrade to DSpace 3.x sche | | PreInit |
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| 4.0 | Initializing from DSpace 4 | 2015-11-20 12:42:52 | Success |
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| 5.0.2014.08.08 | DS-1945 Helpdesk Request a | 2015-11-20 12:42:53 | Success |
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| 5.0.2014.09.25 | DS 1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
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| 5.0.2014.09.26 | DS-1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
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| 5.0.2015.01.27 | MigrateAtmireExtraMetadata | 2015-11-20 12:43:29 | Success |
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| 5.1.2015.12.03 | Atmire CUA 4 migration | 2016-03-21 17:10:41 | Success |
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| 5.1.2015.12.03 | Atmire MQM migration | 2016-03-21 17:10:42 | Success |
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+----------------+----------------------------+---------------------+---------+
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```
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- 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")
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## 2016-08-23
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- Help Paola from CCAFS with her thumbnails again
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- Talk to Atmire about the DSpace 5.5 issue, and it seems to be caused by a bug in FlywayDB
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- They said I should delete the Atmire migrations
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```
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dspacetest=# delete from schema_version where description = 'Atmire CUA 4 migration' and version='5.1.2015.12.03.2';
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dspacetest=# delete from schema_version where description = 'Atmire MQM migration' and version='5.1.2015.12.03.3';
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```
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- After that DSpace starts up by XMLUI now has unrelated issues that I need to solve!
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```
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org.apache.avalon.framework.configuration.ConfigurationException: Type 'ThemeResourceReader' does not exist for 'map:read' at jndi:/localhost/themes/0_CGIAR/sitemap.xmap:136:77
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context:/jndi:/localhost/themes/0_CGIAR/sitemap.xmap - 136:77
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```
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- Looks like we're missing some stuff in the XMLUI module's `sitemap.xmap`, as well as in each of our XMLUI themes
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- Diff them with these to get the `ThemeResourceReader` changes:
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- `dspace-xmlui/src/main/webapp/sitemap.xmap`
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- `dspace-xmlui-mirage2/src/main/webapp/sitemap.xmap`
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- Then we had some NullPointerException from the SolrLogger class, which is apparently part of Atmire's CUA module
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- I tried with a small version bump to CUA but it didn't work (version `5.5-4.1.1-0`)
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- Also, I started looking into huge pages to prepare for PostgreSQL 9.5, but it seems Linode's kernels don't enable them
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## 2016-08-24
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- Clean up and import 48 CCAFS records into DSpace Test
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- 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:
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```
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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).*';
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```
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## 2016-08-25
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- Atmire suggested adding a missing bean to `dspace/config/spring/api/atmire-cua.xml` but it doesn't help:
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```
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...
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Error creating bean with name 'MetadataStorageInfoService'
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...
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```
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- Atmire sent an updated version of `dspace/config/spring/api/atmire-cua.xml` and now XMLUI starts but gives a null pointer exception:
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```
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Java stacktrace: java.lang.NullPointerException
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at org.dspace.app.xmlui.aspect.statistics.Navigation.addOptions(Navigation.java:129)
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at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:228)
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at sun.reflect.GeneratedMethodAccessor126.invoke(Unknown Source)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:606)
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at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
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at com.sun.proxy.$Proxy103.startElement(Unknown Source)
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at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
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at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
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at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
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...
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```
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- Import the 47 CCAFS records to CGSpace, creating the SimpleArchiveFormat bundles and importing like:
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```
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$ ./safbuilder.sh -c /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/3546.csv
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$ 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
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```
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- Finally got DSpace 5.5 working with the Atmire modules after a few rounds of back and forth with Atmire devs
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## 2016-08-26
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- CGSpace had issues tonight, not entirely crashing, but becoming unresponsive
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- The dspace log had this:
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```
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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
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```
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- Related to /rest no doubt
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## 2016-08-27
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- Run corrections for Delia Grace and `CONGO, DR`, and deploy August changes to CGSpace
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- Run all system updates and reboot the server
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