mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2025-01-27 05:49:12 +01:00
Add notes for 2019-05-05
This commit is contained in:
@ -14,12 +14,13 @@ Play with upgrading Mirage 2 dependencies in bower.json because most are several
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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
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bower stuff is a dead end, waste of time, too many issues
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Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of fonts)
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Start working on DSpace 5.1 → 5.5 port:
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Start working on DSpace 5.1 → 5.5 port:
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$ git checkout -b 55new 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.5
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-08/" />
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@ -36,14 +37,15 @@ Play with upgrading Mirage 2 dependencies in bower.json because most are several
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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
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bower stuff is a dead end, waste of time, too many issues
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Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of fonts)
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Start working on DSpace 5.1 → 5.5 port:
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Start working on DSpace 5.1 → 5.5 port:
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$ git checkout -b 55new 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.5
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"/>
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<meta name="generator" content="Hugo 0.55.3" />
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<meta name="generator" content="Hugo 0.55.5" />
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@ -130,13 +132,14 @@ $ git rebase -i dspace-5.5
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<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>
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<li>bower stuff is a dead end, waste of time, too many issues</li>
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<li>Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of <code>fonts</code>)</li>
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<li>Start working on DSpace 5.1 → 5.5 port:</li>
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</ul>
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<li><p>Start working on DSpace 5.1 → 5.5 port:</p>
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<pre><code>$ git checkout -b 55new 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.5
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</code></pre>
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</code></pre></li>
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</ul>
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<ul>
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<li>Lots of conflicts that don’t make sense (ie, shouldn’t conflict!)</li>
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@ -168,11 +171,12 @@ $ git rebase -i dspace-5.5
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<ul>
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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>
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<li>Experiment with fixing more authors, like Delia Grace:</li>
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</ul>
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<li><p>Experiment with fixing more authors, like Delia Grace:</p>
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<pre><code>dspacetest=# update metadatavalue set authority='0b4fcbc1-d930-4319-9b4d-ea1553cca70b', confidence=600 where metadata_field_id=3 and text_value='Grace, D.';
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</code></pre>
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</code></pre></li>
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</ul>
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<h2 id="2016-08-06">2016-08-06</h2>
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@ -194,20 +198,18 @@ $ git rebase -i dspace-5.5
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<li>Ooh, and vanilla DSpace 5.5 works on Tomcat 8 with Java 8!</li>
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<li>Some notes about setting up Tomcat 8, since it’s new on this machine…</li>
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<li>Install latest Oracle Java 8 JDK</li>
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<li>Create <code>setenv.sh</code> in Tomcat 8 <code>libexec/bin</code> directory:
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<br /></li>
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</ul>
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<li><p>Create <code>setenv.sh</code> in Tomcat 8 <code>libexec/bin</code> directory:</p>
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<pre><code>CATALINA_OPTS="-Djava.awt.headless=true -Xms3072m -Xmx3072m -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -Dfile.encoding=UTF-8"
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CATALINA_OPTS="$CATALINA_OPTS -Djava.library.path=/opt/brew/Cellar/tomcat-native/1.2.8/lib"
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JRE_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Edit Tomcat 8 <code>server.xml</code> to add regular HTTP listener for solr</li>
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<li>Symlink webapps:</li>
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</ul>
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<li><p>Edit Tomcat 8 <code>server.xml</code> to add regular HTTP listener for solr</p></li>
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<li><p>Symlink webapps:</p>
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<pre><code>$ rm -rf /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
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$ ln -sv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
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@ -215,7 +217,8 @@ $ ln -sv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/oai
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$ ln -sv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/jspui
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$ ln -sv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/rest
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$ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/solr
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</code></pre>
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</code></pre></li>
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</ul>
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<h2 id="2016-08-09">2016-08-09</h2>
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@ -280,14 +283,13 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
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<ul>
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<li>Fix “CONGO,DR” country name in <code>input-forms.xml</code> (<a href="https://github.com/ilri/DSpace/pull/264">#264</a>)</li>
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<li>Also need to fix existing records using the incorrect form in the database:</li>
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</ul>
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<li><p>Also need to fix existing records using the incorrect form in the database:</p>
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<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';
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</code></pre>
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</code></pre></li>
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<ul>
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<li>I asked a question on the DSpace mailing list about updating “preferred” forms of author names from ORCID</li>
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<li><p>I asked a question on the DSpace mailing list about updating “preferred” forms of author names from ORCID</p></li>
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</ul>
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<h2 id="2016-08-21">2016-08-21</h2>
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@ -303,8 +305,7 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
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<h2 id="2016-08-22">2016-08-22</h2>
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<ul>
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<li>Database migrations are fine on DSpace 5.1:</li>
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</ul>
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<li><p>Database migrations are fine on DSpace 5.1:</p>
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<pre><code>$ ~/dspace/bin/dspace database info
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@ -335,10 +336,9 @@ Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 90
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| 5.1.2015.12.03 | Atmire CUA 4 migration | 2016-03-21 17:10:41 | Success |
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| 5.1.2015.12.03 | Atmire MQM migration | 2016-03-21 17:10:42 | Success |
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+----------------+----------------------------+---------------------+---------+
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</code></pre>
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</code></pre></li>
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<ul>
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<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 “Missing”)</li>
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<li><p>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”)</p></li>
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</ul>
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<h2 id="2016-08-23">2016-08-23</h2>
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@ -346,98 +346,92 @@ Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 90
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<ul>
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<li>Help Paola from CCAFS with her thumbnails again</li>
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<li>Talk to Atmire about the DSpace 5.5 issue, and it seems to be caused by a bug in FlywayDB</li>
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<li>They said I should delete the Atmire migrations
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<br /></li>
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</ul>
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<li><p>They said I should delete the Atmire migrations</p>
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<pre><code>dspacetest=# delete from schema_version where description = 'Atmire CUA 4 migration' and version='5.1.2015.12.03.2';
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dspacetest=# delete from schema_version where description = 'Atmire MQM migration' and version='5.1.2015.12.03.3';
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</code></pre>
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</code></pre></li>
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<ul>
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<li>After that DSpace starts up by XMLUI now has unrelated issues that I need to solve!</li>
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</ul>
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<li><p>After that DSpace starts up by XMLUI now has unrelated issues that I need to solve!</p>
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<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
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context:/jndi:/localhost/themes/0_CGIAR/sitemap.xmap - 136:77
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</code></pre>
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</code></pre></li>
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<ul>
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<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>
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<li>Diff them with these to get the <code>ThemeResourceReader</code> changes:
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<li><p>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</p></li>
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<li><p>Diff them with these to get the <code>ThemeResourceReader</code> changes:</p>
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<ul>
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<li><code>dspace-xmlui/src/main/webapp/sitemap.xmap</code></li>
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<li><code>dspace-xmlui-mirage2/src/main/webapp/sitemap.xmap</code></li>
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</ul></li>
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<li>Then we had some NullPointerException from the SolrLogger class, which is apparently part of Atmire’s CUA module</li>
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<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>
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<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>
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<li><p>Then we had some NullPointerException from the SolrLogger class, which is apparently part of Atmire’s CUA module</p></li>
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<li><p>I tried with a small version bump to CUA but it didn’t work (version <code>5.5-4.1.1-0</code>)</p></li>
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<li><p>Also, I started looking into huge pages to prepare for PostgreSQL 9.5, but it seems Linode’s kernels don’t enable them</p></li>
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</ul>
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<h2 id="2016-08-24">2016-08-24</h2>
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<ul>
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<li>Clean up and import 48 CCAFS records into DSpace Test</li>
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<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>
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</ul>
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<li><p>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:</p>
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<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).*';
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</code></pre>
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</code></pre></li>
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</ul>
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<h2 id="2016-08-25">2016-08-25</h2>
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<ul>
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<li>Atmire suggested adding a missing bean to <code>dspace/config/spring/api/atmire-cua.xml</code> but it doesn’t help:</li>
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</ul>
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<li><p>Atmire suggested adding a missing bean to <code>dspace/config/spring/api/atmire-cua.xml</code> but it doesn’t help:</p>
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<pre><code>...
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Error creating bean with name 'MetadataStorageInfoService'
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...
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Atmire sent an updated version of <code>dspace/config/spring/api/atmire-cua.xml</code> and now XMLUI starts but gives a null pointer exception:</li>
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</ul>
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<li><p>Atmire sent an updated version of <code>dspace/config/spring/api/atmire-cua.xml</code> and now XMLUI starts but gives a null pointer exception:</p>
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<pre><code>Java stacktrace: java.lang.NullPointerException
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at org.dspace.app.xmlui.aspect.statistics.Navigation.addOptions(Navigation.java:129)
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at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:228)
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at sun.reflect.GeneratedMethodAccessor126.invoke(Unknown Source)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:606)
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at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
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at com.sun.proxy.$Proxy103.startElement(Unknown Source)
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at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
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at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
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at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
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at org.dspace.app.xmlui.aspect.statistics.Navigation.addOptions(Navigation.java:129)
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at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:228)
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at sun.reflect.GeneratedMethodAccessor126.invoke(Unknown Source)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:606)
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at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
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at com.sun.proxy.$Proxy103.startElement(Unknown Source)
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at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
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at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
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at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
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...
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Import the 47 CCAFS records to CGSpace, creating the SimpleArchiveFormat bundles and importing like:</li>
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</ul>
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<li><p>Import the 47 CCAFS records to CGSpace, creating the SimpleArchiveFormat bundles and importing like:</p>
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<pre><code>$ ./safbuilder.sh -c /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/3546.csv
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$ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgiar.org/bin/dspace import -a -e aorth@mjanja.ch -c 10568/3546 -s /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/SimpleArchiveFormat -m 3546.map
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Finally got DSpace 5.5 working with the Atmire modules after a few rounds of back and forth with Atmire devs</li>
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<li><p>Finally got DSpace 5.5 working with the Atmire modules after a few rounds of back and forth with Atmire devs</p></li>
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</ul>
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<h2 id="2016-08-26">2016-08-26</h2>
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<ul>
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<li>CGSpace had issues tonight, not entirely crashing, but becoming unresponsive</li>
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<li>The dspace log had this:</li>
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</ul>
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<li><p>The dspace log had this:</p>
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<pre><code>2016-08-26 20:48:05,040 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error - org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Related to /rest no doubt</li>
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<li><p>Related to /rest no doubt</p></li>
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</ul>
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<h2 id="2016-08-27">2016-08-27</h2>
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Reference in New Issue
Block a user