+++ date = "2016-08-01T15:53:00+03:00" author = "Alan Orth" title = "August, 2016" tags = ["notes"] image = "../images/bg.jpg" +++ ## 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 ``` - 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](../images/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](../images/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")