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Add notes for 2021-09-13

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Alan Orth
2021-09-13 16:21:16 +03:00
parent 8b487a4a77
commit c05c7213c2
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@ -42,7 +42,7 @@ $ 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 0.87.0" />
<meta name="generator" content="Hugo 0.88.1" />
@ -137,7 +137,7 @@ $ git rebase -i dspace-5.5
<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
<pre tabindex="0"><code>$ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre><ul>
@ -166,7 +166,7 @@ $ git rebase -i dspace-5.5
<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.';
<pre tabindex="0"><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 &ldquo;View/Open&rdquo; and &ldquo;Bitstreams&rdquo; from the item view</li>
@ -184,7 +184,7 @@ $ git rebase -i dspace-5.5
<li>Install latest Oracle Java 8 JDK</li>
<li>Create <code>setenv.sh</code> in Tomcat 8 <code>libexec/bin</code> directory:</li>
</ul>
<pre><code>CATALINA_OPTS=&quot;-Djava.awt.headless=true -Xms3072m -Xmx3072m -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -Dfile.encoding=UTF-8&quot;
<pre tabindex="0"><code>CATALINA_OPTS=&quot;-Djava.awt.headless=true -Xms3072m -Xmx3072m -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -Dfile.encoding=UTF-8&quot;
CATALINA_OPTS=&quot;$CATALINA_OPTS -Djava.library.path=/opt/brew/Cellar/tomcat-native/1.2.8/lib&quot;
JRE_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home
@ -192,7 +192,7 @@ JRE_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home
<li>Edit Tomcat 8 <code>server.xml</code> to add regular HTTP listener for solr</li>
<li>Symlink webapps:</li>
</ul>
<pre><code>$ rm -rf /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
<pre tabindex="0"><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
@ -246,7 +246,7 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
<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>
</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';
<pre tabindex="0"><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 &ldquo;preferred&rdquo; forms of author names from ORCID</li>
</ul>
@ -262,7 +262,7 @@ $ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/sol
<ul>
<li>Database migrations are fine on DSpace 5.1:</li>
</ul>
<pre><code>$ ~/dspace/bin/dspace database info
<pre tabindex="0"><code>$ ~/dspace/bin/dspace database info
Database URL: jdbc:postgresql://localhost:5432/dspacetest
Database Schema: public
@ -300,12 +300,12 @@ Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 90
<li>Talk to Atmire about the DSpace 5.5 issue, and it seems to be caused by a bug in FlywayDB</li>
<li>They said I should delete the Atmire migrations</li>
</ul>
<pre><code>dspacetest=# delete from schema_version where description = 'Atmire CUA 4 migration' and version='5.1.2015.12.03.2';
<pre tabindex="0"><code>dspacetest=# delete from schema_version where description = 'Atmire CUA 4 migration' and version='5.1.2015.12.03.2';
dspacetest=# delete from schema_version where description = 'Atmire MQM migration' and version='5.1.2015.12.03.3';
</code></pre><ul>
<li>After that DSpace starts up by XMLUI now has unrelated issues that I need to solve!</li>
</ul>
<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
<pre tabindex="0"><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&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>
@ -324,18 +324,18 @@ context:/jndi:/localhost/themes/0_CGIAR/sitemap.xmap - 136:77
<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&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).*';
<pre tabindex="0"><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&rsquo;t help:</li>
</ul>
<pre><code>...
<pre tabindex="0"><code>...
Error creating bean with name 'MetadataStorageInfoService'
...
</code></pre><ul>
<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>
</ul>
<pre><code>Java stacktrace: java.lang.NullPointerException
<pre tabindex="0"><code>Java stacktrace: java.lang.NullPointerException
at org.dspace.app.xmlui.aspect.statistics.Navigation.addOptions(Navigation.java:129)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:228)
at sun.reflect.GeneratedMethodAccessor126.invoke(Unknown Source)
@ -350,7 +350,7 @@ Error creating bean with name 'MetadataStorageInfoService'
</code></pre><ul>
<li>Import the 47 CCAFS records to CGSpace, creating the SimpleArchiveFormat bundles and importing like:</li>
</ul>
<pre><code>$ ./safbuilder.sh -c /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/3546.csv
<pre tabindex="0"><code>$ ./safbuilder.sh -c /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/3546.csv
$ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /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
</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>
@ -360,7 +360,7 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<li>CGSpace had issues tonight, not entirely crashing, but becoming unresponsive</li>
<li>The dspace log had this:</li>
</ul>
<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
<pre tabindex="0"><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
</code></pre><ul>
<li>Related to /rest no doubt</li>
</ul>