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Add notes for 2019-12-17

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Alan Orth
2019-12-17 14:49:24 +02:00
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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 0.60.1" />
<meta name="generator" content="Hugo 0.61.0" />
@ -120,7 +120,7 @@ $ git rebase -i dspace-5.5
</p>
</header>
<h2 id="20160801">2016-08-01</h2>
<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>
@ -141,33 +141,33 @@ $ git rebase -i dspace-5.5
<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="20160802">2016-08-02</h2>
<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="20160804">2016-08-04</h2>
<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="20160805">2016-08-05</h2>
<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="20160806">2016-08-06</h2>
</code></pre><h2 id="2016-08-06">2016-08-06</h2>
<ul>
<li>Finally figured out how to remove &ldquo;View/Open&rdquo; and &ldquo;Bitstreams&rdquo; from the item view</li>
</ul>
<h2 id="20160807">2016-08-07</h2>
<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="20160808">2016-08-08</h2>
<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&hellip;</li>
@ -190,13 +190,13 @@ $ 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="20160809">2016-08-09</h2>
</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="20160810">2016-08-10</h2>
<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>
@ -204,27 +204,27 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
<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>
</ul>
<h2 id="20160811">2016-08-11</h2>
<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="/cgspace-notes/2016/08/dspace55-ubuntu16.04.png" alt="DSpace 5.5 on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5"></p>
<h2 id="20160814">2016-08-14</h2>
<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="20160815">2016-08-15</h2>
<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="/cgspace-notes/2016/08/nodejs-nginx.png" alt="ExpressJS running behind nginx"></p>
<h2 id="20160816">2016-08-16</h2>
<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="20160817">2016-08-17</h2>
<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>
@ -233,7 +233,7 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
<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="20160818">2016-08-18</h2>
<h2 id="2016-08-18">2016-08-18</h2>
<ul>
<li>Fix &ldquo;CONGO,DR&rdquo; 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>
@ -242,7 +242,7 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
</code></pre><ul>
<li>I asked a question on the DSpace mailing list about updating &ldquo;preferred&rdquo; forms of author names from ORCID</li>
</ul>
<h2 id="20160821">2016-08-21</h2>
<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>
@ -250,7 +250,7 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
<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>
<h2 id="20160822">2016-08-22</h2>
<h2 id="2016-08-22">2016-08-22</h2>
<ul>
<li>Database migrations are fine on DSpace 5.1:</li>
</ul>
@ -286,7 +286,7 @@ Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 90
</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>
</ul>
<h2 id="20160823">2016-08-23</h2>
<h2 id="2016-08-23">2016-08-23</h2>
<ul>
<li>Help Paola from CCAFS with her thumbnails again</li>
<li>Talk to Atmire about the DSpace 5.5 issue, and it seems to be caused by a bug in FlywayDB</li>
@ -311,13 +311,13 @@ context:/jndi:/localhost/themes/0_CGIAR/sitemap.xmap - 136:77
<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>
</ul>
<h2 id="20160824">2016-08-24</h2>
<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>
</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="20160825">2016-08-25</h2>
</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>
</ul>
@ -347,7 +347,7 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
</code></pre><ul>
<li>Finally got DSpace 5.5 working with the Atmire modules after a few rounds of back and forth with Atmire devs</li>
</ul>
<h2 id="20160826">2016-08-26</h2>
<h2 id="2016-08-26">2016-08-26</h2>
<ul>
<li>CGSpace had issues tonight, not entirely crashing, but becoming unresponsive</li>
<li>The dspace log had this:</li>
@ -356,7 +356,7 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
</code></pre><ul>
<li>Related to /rest no doubt</li>
</ul>
<h2 id="20160827">2016-08-27</h2>
<h2 id="2016-08-27">2016-08-27</h2>
<ul>
<li>Run corrections for Delia Grace and <code>CONGO, DR</code>, and deploy August changes to CGSpace</li>
<li>Run all system updates and reboot the server</li>