<!DOCTYPE html> <html lang="en-us"> <head prefix="og: http://ogp.me/ns#"> <meta charset="utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1" /> <meta property="og:title" content=" August, 2016 · CGSpace Notes" /> <meta property="og:site_name" content="CGSpace Notes" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-08/" /> <meta property="og:type" content="article" /> <meta property="og:article:published_time" content="2016-08-01T15:53:00+03:00" /> <meta property="og:article:tag" content="notes" /> <title> August, 2016 · CGSpace Notes </title> <link rel="stylesheet" href="https://alanorth.github.io/cgspace-notes/css/bootstrap.min.css" /> <link rel="stylesheet" href="https://alanorth.github.io/cgspace-notes/css/main.css" /> <link rel="stylesheet" href="https://alanorth.github.io/cgspace-notes/css/font-awesome.min.css" /> <link rel="stylesheet" href="https://alanorth.github.io/cgspace-notes/css/github.css" /> <link rel="stylesheet" href="//fonts.googleapis.com/css?family=Source+Sans+Pro:200,300,400" type="text/css"> <link rel="shortcut icon" href="https://alanorth.github.io/cgspace-notes/images/favicon.ico" /> <link rel="apple-touch-icon" href="https://alanorth.github.io/cgspace-notes/images/apple-touch-icon.png" /> </head> <body> <header class="global-header" style="background-image:url(../images/bg.jpg )"> <section class="header-text"> <h1><a href="https://alanorth.github.io/cgspace-notes/">CGSpace Notes</a></h1> <div class="sns-links hidden-print"> </div> <a href="https://alanorth.github.io/cgspace-notes/" class="btn-header btn-back hidden-xs"> <i class="fa fa-angle-left" aria-hidden="true"></i> Home </a> </section> </header> <main class="container"> <article> <header> <h1 class="text-primary">August, 2016</h1> <div class="post-meta clearfix"> <div class="post-date pull-left"> Posted on <time datetime="2016-08-01T15:53:00+03:00"> Aug 1, 2016 </time> </div> <div class="pull-right"> <span class="post-tag small"><a href="https://alanorth.github.io/cgspace-notes//tags/notes">#notes</a></span> </div> </div> </header> <section> <h2 id="2016-08-01">2016-08-01</h2> <ul> <li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li> <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 → 5.5 port:</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> </ul> <h2 id="2016-08-02">2016-08-02</h2> <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> </ul> <h2 id="2016-08-04">2016-08-04</h2> <ul> <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> </ul> <h2 id="2016-08-05">2016-08-05</h2> <ul> <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> <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> <h2 id="2016-08-07">2016-08-07</h2> <ul> <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> <h2 id="2016-08-09">2016-08-09</h2> <ul> <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> </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> </ul> <h2 id="2016-08-11">2016-08-11</h2> <ul> <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> <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> </ul> <h2 id="2016-08-15">2016-08-15</h2> <ul> <li>Notes on NodeJS + nginx + systemd: <a href="https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1">https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1</a></li> </ul> <p><img src="../images/2016/08/nodejs-nginx.png" alt="ExpressJS running behind nginx" /></p> <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> </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> </ul> <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> <ul> <li>I asked a question on the DSpace mailing list about updating “preferred” forms of author names from ORCID</li> </ul> <h2 id="2016-08-21">2016-08-21</h2> <ul> <li>A few days ago someone on the DSpace mailing list suggested I try <code>dspace dsrun org.dspace.authority.UpdateAuthorities</code> to update preferred author names from ORCID</li> <li>If you set <code>auto-update-items=true</code> in <code>dspace/config/modules/solrauthority.cfg</code> it is supposed to update records it finds automatically</li> <li>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</li> <li>Still troubleshooting Atmire modules on DSpace 5.5</li> <li>I sent them some new verbose logs: <a href="https://gist.github.com/alanorth/700748995649688148ceba89d760253e">https://gist.github.com/alanorth/700748995649688148ceba89d760253e</a></li> </ul> </section> <footer> <section class="author-info row"> <div class="author-avatar col-md-2"> </div> <div class="author-meta col-md-6"> <h1 class="author-name text-primary">Alan Orth</h1> </div> </section> <ul class="pager"> <li class="previous"><a href="https://alanorth.github.io/cgspace-notes/2016-07/"><span aria-hidden="true">←</span> Older</a></li> <li class="next disabled"><a href="#">Newer <span aria-hidden="true">→</span></a></li> </ul> </footer> </article> </main> <footer class="container global-footer"> <div class="copyright-note pull-left"> </div> <div class="sns-links hidden-print"> </div> </footer> <script src="https://alanorth.github.io/cgspace-notes/js/highlight.pack.js"></script> <script> hljs.initHighlightingOnLoad(); </script> </body> </html>