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August, 2016 · CGSpace Notes
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< h1 class = "text-primary" > August, 2016< / h1 >
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< span class = "post-tag small" > < a href = "https://alanorth.github.io/cgspace-notes//tags/notes" > #notes< / a > < / span >
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< h2 id = "2016-08-01" > 2016-08-01< / h2 >
2016-08-01 14:45:50 +02:00
< ul >
< li > Add updated distribution license from Sisay (< a href = "https://github.com/ilri/DSpace/issues/259" > #259< / a > )< / li >
2016-08-02 00:06:47 +02:00
< li > Play with upgrading Mirage 2 dependencies in < code > bower.json< / code > because most are several versions of out date< / li >
< li > 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< / li >
< li > bower stuff is a dead end, waste of time, too many issues< / li >
< li > Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of < code > fonts< / code > )< / li >
< li > Start working on DSpace 5.1 < / li >
< / ul >
< pre > < code > $ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
< / code > < / pre >
< ul >
< li > Lots of conflicts that don’ t make sense (ie, shouldn’ t conflict!)< / li >
< li > This file in particular conflicts almost 10 times: < code > dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss< / code > < / li >
< li > Checking out a clean branch at 5.5 and cherry-picking our commits works where that file would normally have a conflict< / li >
< li > Seems to be related to merge commits< / li >
< li > < code > git rebase --preserve-merges< / code > doesn’ t seem to help< / li >
< li > Eventually I just turned on git rerere and solved the conflicts and completed the 403 commit rebase< / li >
< li > The 5.5 code now builds but doesn’ t run (white page in Tomcat)< / li >
2016-08-02 14:03:28 +02:00
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< h2 id = "2016-08-02" > 2016-08-02< / h2 >
2016-08-02 14:03:28 +02:00
< ul >
< li > Ask Atmire for help with DSpace 5.5 issue< / li >
< li > Vanilla DSpace 5.5 deploys and runs fine< / li >
< li > Playing with DSpace in Ubuntu 16.04 and Tomcat 7< / li >
< li > Everything is still fucked up, even vanilla DSpace 5.5< / li >
2016-08-05 13:05:32 +02:00
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< h2 id = "2016-08-04" > 2016-08-04< / h2 >
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< li > Ask on DSpace mailing list about duplicate authors, Discovery and author text values< / li >
< li > Atmire responded with some new DSpace 5.5 ready versions to try for their modules< / li >
2016-08-01 14:45:50 +02:00
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2016-08-05 15:38:43 +02:00
< h2 id = "2016-08-05" > 2016-08-05< / h2 >
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< li > Fix item display incorrectly displaying Species when Breeds were present (< a href = "https://github.com/ilri/DSpace/pull/260" > #260< / a > )< / li >
< li > Experiment with fixing more authors, like Delia Grace:< / li >
< / ul >
< pre > < code > dspacetest=# update metadatavalue set authority='0b4fcbc1-d930-4319-9b4d-ea1553cca70b', confidence=600 where metadata_field_id=3 and text_value='Grace, D.';
< / code > < / pre >
2016-08-06 15:55:17 +02:00
< h2 id = "2016-08-06" > 2016-08-06< / h2 >
< ul >
< li > Finally figured out how to remove “ View/Open” and “ Bitstreams” from the item view< / li >
< / ul >
2016-08-08 22:22:50 +02:00
< h2 id = "2016-08-07" > 2016-08-07< / h2 >
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< li > Start working on Ubuntu 16.04 Ansible playbook for Tomcat 8, PostgreSQL 9.5, Oracle 8, etc< / li >
< / ul >
< h2 id = "2016-08-08" > 2016-08-08< / h2 >
< ul >
< li > Still troubleshooting Atmire modules on DSpace 5.5< / li >
< li > Vanilla DSpace 5.5 works on Tomcat 7… < / li >
< li > Ooh, and vanilla DSpace 5.5 works on Tomcat 8 with Java 8!< / li >
< li > Some notes about setting up Tomcat 8, since it’ s new on this machine… < / li >
< li > Install latest Oracle Java 8 JDK< / li >
< li > Create < code > setenv.sh< / code > in Tomcat 8 < code > libexec/bin< / code > directory:
< br / > < / li >
< / ul >
< pre > < code > 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
< / code > < / pre >
< ul >
< li > Edit Tomcat 8 < code > server.xml< / code > to add regular HTTP listener for solr< / li >
< li > Symlink webapps:< / li >
< / ul >
< pre > < code > $ 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
< / code > < / pre >
2016-08-09 11:31:06 +02:00
< h2 id = "2016-08-09" > 2016-08-09< / h2 >
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< li > More tests of Atmire’ s 5.5 modules on a clean, working instance of < code > 5_x-prod< / code > < / li >
< li > Still fails, though perhaps differently than before (Flyway): < a href = "https://gist.github.com/alanorth/5d49c45a16efd7c6bc1e6642e66118b2" > https://gist.github.com/alanorth/5d49c45a16efd7c6bc1e6642e66118b2< / a > < / li >
< li > More work on Tomcat 8 and Java 8 stuff for Ansible playbooks< / li >
2016-08-10 12:19:46 +02:00
< / ul >
< h2 id = "2016-08-10" > 2016-08-10< / h2 >
< ul >
< li > Turns out DSpace 5.x isn’ t ready for Tomcat 8: < a href = "https://jira.duraspace.org/browse/DS-3092" > https://jira.duraspace.org/browse/DS-3092< / a > < / li >
< li > So we’ ll need to use Tomcat 7 + Java 8 on Ubuntu 16.04< / li >
< li > More work on the Ansible stuff for this, allowing Tomcat 7 to use Java 8< / li >
< li > Merge pull request for fixing the type Discovery index to use < code > dc.type< / code > (< a href = "https://github.com/ilri/DSpace/pull/262" > #262< / a > )< / li >
< li > Merge pull request for removing “ Bitstream” text from item display, as it confuses users and isn’ t necessary (< a href = "https://github.com/ilri/DSpace/pull/263" > #263< / a > )< / li >
2016-08-09 11:31:06 +02:00
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2016-08-11 07:50:33 +02:00
< h2 id = "2016-08-11" > 2016-08-11< / h2 >
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< li > Finally got DSpace (5.5) running on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5 via the updated Ansible stuff< / li >
< / ul >
< p > < img src = "../images/2016/08/dspace55-ubuntu16.04.png" alt = "DSpace 5.5 on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5" / > < / p >
2016-08-15 10:34:55 +02:00
< h2 id = "2016-08-14" > 2016-08-14< / h2 >
< ul >
< li > Update Mirage 2 build notes for Ubuntu 16.04: < a href = "https://gist.github.com/alanorth/2cf9c15834dc68a514262fcb04004cb0" > https://gist.github.com/alanorth/2cf9c15834dc68a514262fcb04004cb0< / a > < / li >
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< h2 id = "2016-08-15" > 2016-08-15< / h2 >
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< li > Notes on NodeJS + nginx + systemd: < a href = "https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1" > https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1< / a > < / li >
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< p > < img src = "../images/2016/08/nodejs-nginx.png" alt = "ExpressJS running behind nginx" / > < / p >
2016-08-17 06:19:11 +02:00
< h2 id = "2016-08-16" > 2016-08-16< / h2 >
< ul >
< li > Troubleshoot Paramiko connection issues with Ansible on ILRI servers: < a href = "https://github.com/ilri/rmg-ansible-public/issues/37" > #37< / a > < / li >
< li > Turns out we need to add some MACs to our < code > sshd_config< / code > : hmac-sha2-512,hmac-sha2-256< / li >
< li > Update DSpace Test’ s Java to version 8 to start testing this configuration (< a href = "https://wiki.apache.org/solr/ShawnHeisey" > seeing as Solr recommends it< / a > )< / li >
2016-08-17 13:40:16 +02:00
< / ul >
< h2 id = "2016-08-17" > 2016-08-17< / h2 >
< ul >
< li > More work on Let’ s Encrypt stuff for Ansible roles< / li >
< li > Yesterday Atmire responded about DSpace 5.5 issues and asked me to try the < code > dspace database repair< / code > command to fix Flyway issues< / li >
< li > The < code > dspace database< / code > command doesn’ t even run: < a href = "https://gist.github.com/alanorth/c43c8d89e8df346d32c0ee938be90cd5" > https://gist.github.com/alanorth/c43c8d89e8df346d32c0ee938be90cd5< / a > < / li >
< li > Oops, it looks like the missing classes causing < code > dspace database< / code > to fail were coming from the old < code > ~/dspace/config/spring< / code > folder< / li >
< li > After removing the spring folder and running ant install again, < code > dspace database< / code > works< / li >
< li > I see there are missing and pending Flyway migrations, but running < code > dspace database repair< / code > and < code > dspace database migrate< / code > does nothing: < a href = "https://gist.github.com/alanorth/41ed5abf2ff32d8ac9eedd1c3d015d70" > https://gist.github.com/alanorth/41ed5abf2ff32d8ac9eedd1c3d015d70< / a > < / li >
2016-08-17 06:19:11 +02:00
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2016-08-18 14:48:32 +02:00
< h2 id = "2016-08-18" > 2016-08-18< / h2 >
< ul >
< li > Fix “ CONGO,DR” country name in < code > input-forms.xml< / code > (< a href = "https://github.com/ilri/DSpace/pull/264" > #264< / a > )< / li >
< li > Also need to fix existing records using the incorrect form in the database:< / li >
< / ul >
< pre > < code > dspace=# update metadatavalue set text_value='CONGO, DR' where resource_type_id=2 and metadata_field_id=228 and text_value='CONGO,DR';
< / code > < / pre >
2016-08-18 15:35:08 +02:00
< ul >
< li > I asked a question on the DSpace mailing list about updating “ preferred” forms of author names from ORCID< / li >
< / ul >
2016-08-01 14:45:50 +02:00
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