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@ -39,7 +39,7 @@ $ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
"/>
<meta name="generator" content="Hugo 0.62.2" />
<meta name="generator" content="Hugo 0.63.1" />
@ -69,7 +69,7 @@ $ git rebase -i dspace-5.5
<!-- combined, minified CSS -->
<link href="https://alanorth.github.io/cgspace-notes/css/style.a20c1a4367639632cdb341d23c27ca44fedcc75b0f8b3cbea6203010da153d3c.css" rel="stylesheet" integrity="sha256-ogwaQ2djljLNs0HSPCfKRP7cx1sPizy&#43;piAwENoVPTw=" crossorigin="anonymous">
<link href="https://alanorth.github.io/cgspace-notes/css/style.23e2c3298bcc8c1136c19aba330c211ec94c36f7c4454ea15cf4d3548370042a.css" rel="stylesheet" integrity="sha256-I&#43;LDKYvMjBE2wZq6MwwhHslMNvfERU6hXPTTVINwBCo=" crossorigin="anonymous">
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@ -117,7 +117,7 @@ $ git rebase -i dspace-5.5
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-08/">August, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-08-01T15:53:00&#43;03:00">Mon Aug 01, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
@ -134,13 +134,13 @@ $ git rebase -i dspace-5.5
$ 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>Lots of conflicts that don&rsquo;t make sense (ie, shouldn&rsquo;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><code>git rebase --preserve-merges</code> doesn&rsquo;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>
<li>The 5.5 code now builds but doesn&rsquo;t run (white page in Tomcat)</li>
</ul>
<h2 id="2016-08-02">2016-08-02</h2>
<ul>
@ -173,7 +173,7 @@ $ git rebase -i dspace-5.5
<li>Still troubleshooting Atmire modules on DSpace 5.5</li>
<li>Vanilla DSpace 5.5 works on Tomcat 7&hellip;</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&hellip;</li>
<li>Some notes about setting up Tomcat 8, since it&rsquo;s new on this machine&hellip;</li>
<li>Install latest Oracle Java 8 JDK</li>
<li>Create <code>setenv.sh</code> in Tomcat 8 <code>libexec/bin</code> directory:</li>
</ul>
@ -193,17 +193,17 @@ $ ln -sv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/res
$ 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>More tests of Atmire&rsquo;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>Turns out DSpace 5.x isn&rsquo;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&rsquo;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 &ldquo;Bitstream&rdquo; text from item display, as it confuses users and isn't necessary (<a href="https://github.com/ilri/DSpace/pull/263">#263</a>)</li>
<li>Merge pull request for removing &ldquo;Bitstream&rdquo; text from item display, as it confuses users and isn&rsquo;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>
@ -223,13 +223,13 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
<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>
<li>Update DSpace Test&rsquo;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>More work on Let&rsquo;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>The <code>dspace database</code> command doesn&rsquo;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>
@ -247,7 +247,7 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
<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>I updated my name format on ORCID and I&rsquo;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>
@ -285,7 +285,7 @@ Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 90
| 5.1.2015.12.03 | Atmire MQM migration | 2016-03-21 17:10:42 | Success |
+----------------+----------------------------+---------------------+---------+
</code></pre><ul>
<li>So I'm not sure why they have problems when we move to DSpace 5.5 (even the 5.1 migrations themselves show as &ldquo;Missing&rdquo;)</li>
<li>So I&rsquo;m not sure why they have problems when we move to DSpace 5.5 (even the 5.1 migrations themselves show as &ldquo;Missing&rdquo;)</li>
</ul>
<h2 id="2016-08-23">2016-08-23</h2>
<ul>
@ -301,26 +301,26 @@ dspacetest=# delete from schema_version where description = 'Atmire MQM migrati
<pre><code>org.apache.avalon.framework.configuration.ConfigurationException: Type 'ThemeResourceReader' does not exist for 'map:read' at jndi:/localhost/themes/0_CGIAR/sitemap.xmap:136:77
context:/jndi:/localhost/themes/0_CGIAR/sitemap.xmap - 136:77
</code></pre><ul>
<li>Looks like we're missing some stuff in the XMLUI module's <code>sitemap.xmap</code>, as well as in each of our XMLUI themes</li>
<li>Looks like we&rsquo;re missing some stuff in the XMLUI module&rsquo;s <code>sitemap.xmap</code>, as well as in each of our XMLUI themes</li>
<li>Diff them with these to get the <code>ThemeResourceReader</code> changes:
<ul>
<li><code>dspace-xmlui/src/main/webapp/sitemap.xmap</code></li>
<li><code>dspace-xmlui-mirage2/src/main/webapp/sitemap.xmap</code></li>
</ul>
</li>
<li>Then we had some NullPointerException from the SolrLogger class, which is apparently part of Atmire's CUA module</li>
<li>I tried with a small version bump to CUA but it didn't work (version <code>5.5-4.1.1-0</code>)</li>
<li>Also, I started looking into huge pages to prepare for PostgreSQL 9.5, but it seems Linode's kernels don't enable them</li>
<li>Then we had some NullPointerException from the SolrLogger class, which is apparently part of Atmire&rsquo;s CUA module</li>
<li>I tried with a small version bump to CUA but it didn&rsquo;t work (version <code>5.5-4.1.1-0</code>)</li>
<li>Also, I started looking into huge pages to prepare for PostgreSQL 9.5, but it seems Linode&rsquo;s kernels don&rsquo;t enable them</li>
</ul>
<h2 id="2016-08-24">2016-08-24</h2>
<ul>
<li>Clean up and import 48 CCAFS records into DSpace Test</li>
<li>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:</li>
<li>SQL to get all journal titles from dc.source (55), since it&rsquo;s apparently used for internal DSpace filename shit, but we moved all our journal titles there a few months ago:</li>
</ul>
<pre><code>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).*';
</code></pre><h2 id="2016-08-25">2016-08-25</h2>
<ul>
<li>Atmire suggested adding a missing bean to <code>dspace/config/spring/api/atmire-cua.xml</code> but it doesn't help:</li>
<li>Atmire suggested adding a missing bean to <code>dspace/config/spring/api/atmire-cua.xml</code> but it doesn&rsquo;t help:</li>
</ul>
<pre><code>...
Error creating bean with name 'MetadataStorageInfoService'