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April, 2016 &middot; CGSpace Notes
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<h1><a href="/cgspace-notes/">CGSpace Notes</a></h1>
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<h1 class="text-primary">April, 2016</h1>
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Posted on
<time datetime="2016-04-04T11:06:00&#43;03:00">
Apr 4, 2016
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<span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span>
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<h2 id="2016-04-04:c88be15f5b2f07c85f7742556a955e47">2016-04-04</h2>
<ul>
<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
<li>We are backing up all logs in the log folder, including useless stuff like solr, cocoon, handle-plugin, etc</li>
<li>After running DSpace for over five years I&rsquo;ve never needed to look in any other log file than dspace.log, leave alone one from last year!</li>
<li>This will save us a few gigs of backup space we&rsquo;re paying for on S3</li>
<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
</ul>
<pre><code>Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.&lt;init&gt;(FileInputStream.java:146)
at edu.sdsc.grid.io.local.LocalFileInputStream.open(LocalFileInputStream.java:171)
at edu.sdsc.grid.io.GeneralFileInputStream.&lt;init&gt;(GeneralFileInputStream.java:145)
at edu.sdsc.grid.io.local.LocalFileInputStream.&lt;init&gt;(LocalFileInputStream.java:139)
at edu.sdsc.grid.io.FileFactory.newFileInputStream(FileFactory.java:630)
at org.dspace.storage.bitstore.BitstreamStorageManager.retrieve(BitstreamStorageManager.java:525)
at org.dspace.checker.BitstreamDAO.getBitstream(BitstreamDAO.java:60)
at org.dspace.checker.CheckerCommand.processBitstream(CheckerCommand.java:303)
at org.dspace.checker.CheckerCommand.checkBitstream(CheckerCommand.java:171)
at org.dspace.checker.CheckerCommand.process(CheckerCommand.java:120)
at org.dspace.app.checker.ChecksumChecker.main(ChecksumChecker.java:236)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:225)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:77)
******************************************************
</code></pre>
<ul>
<li>So this would be the <code>tomcat7</code> Unix user, who seems to have a default limit of 1024 files in its shell</li>
<li>For what it&rsquo;s worth, we have been setting the actual Tomcat 7 process&rsquo; limit to 16384 for a few years (in <code>/etc/default/tomcat7</code>)</li>
<li>Looks like cron will read limits from <code>/etc/security/limits.*</code> so we can do something for the tomcat7 user there</li>
<li>Submit pull request for Tomcat 7 limits in Ansible dspace role (<a href="https://github.com/ilri/rmg-ansible-public/pull/30">#30</a>)</li>
</ul>
<h2 id="2016-04-05:c88be15f5b2f07c85f7742556a955e47">2016-04-05</h2>
<ul>
<li>Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don&rsquo;t need!</li>
</ul>
<pre><code># s3cmd ls s3://cgspace.cgiar.org/log/ &gt; /tmp/s3-logs.txt
# grep checker.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep cocoon.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep handle-plugin.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep solr.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
</code></pre>
<ul>
<li>Also, adjust the cron jobs for backups so they only backup <code>dspace.log</code> and some stats files (.dat)</li>
<li>Try to do some metadata field migrations using the Atmire batch UI (<code>dc.Species</code> → <code>cg.species</code>) but it took several hours and even missed a few records</li>
</ul>
<h2 id="2016-04-06:c88be15f5b2f07c85f7742556a955e47">2016-04-06</h2>
<ul>
<li>A better way to move metadata on this scale is via SQL, for example <code>dc.type.output</code> → <code>dc.type</code> (their IDs in the metadatafieldregistry are 66 and 109, respectively):</li>
</ul>
<pre><code>dspacetest=# update metadatavalue set metadata_field_id=109 where metadata_field_id=66;
UPDATE 40852
</code></pre>
<ul>
<li>After that an <code>index-discovery -bf</code> is required</li>
<li>Start working on metadata migrations, add 25 or so new metadata fields to CGSpace</li>
</ul>
<h2 id="2016-04-07:c88be15f5b2f07c85f7742556a955e47">2016-04-07</h2>
<ul>
<li>Write shell script to do the migration of fields: <a href="https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b">https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b</a></li>
<li>Testing with a few fields it seems to work well:</li>
</ul>
<pre><code>$ ./migrate-fields.sh
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
UPDATE 40883
UPDATE metadatavalue SET metadata_field_id=202 WHERE metadata_field_id=72
UPDATE 21420
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
UPDATE 51258
</code></pre>
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<h1 class="author-name text-primary">Alan Orth</h1>
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