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April, 2016 · 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
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<time datetime="2016-04-04T11:06:00+03:00">
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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>
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<ul>
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<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
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<li>We are backing up all logs in the log folder, including useless stuff like solr, cocoon, handle-plugin, etc</li>
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<li>After running DSpace for over five years I’ve never needed to look in any other log file than dspace.log, leave alone one from last year!</li>
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<li>This will save us a few gigs of backup space we’re paying for on S3</li>
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<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
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</ul>
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<pre><code>Run start time: 03/06/2016 04:00:22
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Error retrieving bitstream ID 71274 from asset store.
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java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
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at java.io.FileInputStream.open(Native Method)
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at java.io.FileInputStream.<init>(FileInputStream.java:146)
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at edu.sdsc.grid.io.local.LocalFileInputStream.open(LocalFileInputStream.java:171)
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at edu.sdsc.grid.io.GeneralFileInputStream.<init>(GeneralFileInputStream.java:145)
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at edu.sdsc.grid.io.local.LocalFileInputStream.<init>(LocalFileInputStream.java:139)
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at edu.sdsc.grid.io.FileFactory.newFileInputStream(FileFactory.java:630)
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at org.dspace.storage.bitstore.BitstreamStorageManager.retrieve(BitstreamStorageManager.java:525)
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at org.dspace.checker.BitstreamDAO.getBitstream(BitstreamDAO.java:60)
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at org.dspace.checker.CheckerCommand.processBitstream(CheckerCommand.java:303)
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at org.dspace.checker.CheckerCommand.checkBitstream(CheckerCommand.java:171)
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at org.dspace.checker.CheckerCommand.process(CheckerCommand.java:120)
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at org.dspace.app.checker.ChecksumChecker.main(ChecksumChecker.java:236)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
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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.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:225)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:77)
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******************************************************
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</code></pre>
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<ul>
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<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>
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<li>For what it’s worth, we have been setting the actual Tomcat 7 process’ limit to 16384 for a few years (in <code>/etc/default/tomcat7</code>)</li>
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<li>Looks like cron will read limits from <code>/etc/security/limits.*</code> so we can do something for the tomcat7 user there</li>
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<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>
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</ul>
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<h2 id="2016-04-05:c88be15f5b2f07c85f7742556a955e47">2016-04-05</h2>
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<ul>
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<li>Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don’t need!</li>
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</ul>
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<pre><code># s3cmd ls s3://cgspace.cgiar.org/log/ > /tmp/s3-logs.txt
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# grep checker.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
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# grep cocoon.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
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# grep handle-plugin.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
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# grep solr.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
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</code></pre>
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<ul>
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<li>Also, adjust the cron jobs for backups so they only backup <code>dspace.log</code> and some stats files (.dat)</li>
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<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>
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</ul>
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<h2 id="2016-04-06:c88be15f5b2f07c85f7742556a955e47">2016-04-06</h2>
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<ul>
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<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>
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</ul>
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<pre><code>dspacetest=# update metadatavalue set metadata_field_id=109 where metadata_field_id=66;
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UPDATE 40852
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</code></pre>
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<ul>
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<li>After that an <code>index-discovery -bf</code> is required</li>
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<li>Start working on metadata migrations, add 25 or so new metadata fields to CGSpace</li>
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</ul>
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<h2 id="2016-04-07:c88be15f5b2f07c85f7742556a955e47">2016-04-07</h2>
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<ul>
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<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>
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<li>Testing with a few fields it seems to work well:</li>
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</ul>
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<pre><code>$ ./migrate-fields.sh
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UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
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UPDATE 40883
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UPDATE metadatavalue SET metadata_field_id=202 WHERE metadata_field_id=72
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UPDATE 21420
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UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
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UPDATE 51258
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</code></pre>
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<h2 id="2016-04-08:c88be15f5b2f07c85f7742556a955e47">2016-04-08</h2>
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<ul>
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<li>Discuss metadata renaming with Abenet, we decided it’s better to start with the center-specific subjects like ILRI, CIFOR, CCAFS, IWMI, and CPWF</li>
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<li>I’ve e-mailed CCAFS and CPWF people to ask them how much time it will take for them to update their systems to cope with this change</li>
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</ul>
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<h2 id="2016-04-10:c88be15f5b2f07c85f7742556a955e47">2016-04-10</h2>
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<ul>
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<li>Looking at the DOI issue <a href="https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=678507860">reported by Leroy from CIAT a few weeks ago</a></li>
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<li>It seems the <code>dx.doi.org</code> URLs are much more proper in our repository!</li>
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</ul>
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<pre><code>dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and text_value like 'http://dx.doi.org%';
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count
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-------
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5638
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(1 row)
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dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and text_value like 'http://doi.org%';
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count
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-------
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3
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</code></pre>
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<ul>
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<li>I will manually edit the <code>dc.identifier.doi</code> in <a href="https://cgspace.cgiar.org/handle/10568/72509?show=full"><sup>10568</sup>⁄<sub>72509</sub></a> and tweet the link, then check back in a week to see if the donut gets updated</li>
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</ul>
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<h2 id="2016-04-11:c88be15f5b2f07c85f7742556a955e47">2016-04-11</h2>
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<ul>
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<li>The donut is already updated and shows the correct number now</li>
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<li>CCAFS people say it will only take them an hour to update their code for the metadata renames, so I proposed we’d do it tentatively on Monday the 18th.</li>
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</ul>
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<h2 id="2016-04-12:c88be15f5b2f07c85f7742556a955e47">2016-04-12</h2>
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<ul>
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<li>Looking at quality of WLE data (<code>cg.subject.iwmi</code>) in SQL:</li>
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</ul>
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<pre><code>dspacetest=# select text_value, count(*) from metadatavalue where metadata_field_id=217 group by text_value order by count(*) desc;
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</code></pre>
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<ul>
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<li>Listings and Reports is still not returning reliable data for <code>dc.type</code></li>
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<li>I think we need to ask Atmire, as their documentation isn’t too clear on the format of the filter configs</li>
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<li>Alternatively, I want to see if I move all the data from <code>dc.type.output</code> to <code>dc.type</code> and then re-index, if it behaves better</li>
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<li>Looking at our <code>input-forms.xml</code> I see we have two sets of ILRI subjects, but one has a few extra subjects</li>
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<li>Remove one set of ILRI subjects and remove duplicate <code>VALUE CHAINS</code> from existing list (<a href="https://github.com/ilri/DSpace/pull/216">#216</a>)</li>
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<li>I decided to keep the set of subjects that had <code>FMD</code> and <code>RANGELANDS</code> added, as it appears to have been requested to have been added, and might be the newer list</li>
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<li>I found 226 blank metadatavalues:</li>
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</ul>
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<pre><code>dspacetest# select * from metadatavalue where resource_type_id=2 and text_value='';
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</code></pre>
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<ul>
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<li>I think we should delete them and do a full re-index:</li>
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</ul>
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<pre><code>dspacetest=# delete from metadatavalue where resource_type_id=2 and text_value='';
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DELETE 226
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</code></pre>
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<ul>
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<li>I deleted them on CGSpace but I’ll wait to do the re-index as we’re going to be doing one in a few days for the metadata changes anyways</li>
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<li>In other news, moving the <code>dc.type.output</code> to <code>dc.type</code> and re-indexing seems to have fixed the Listings and Reports issue from above</li>
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<li>Unfortunately this isn’t a very good solution, because Listings and Reports config should allow us to filter on <code>dc.type.*</code> but the documentation isn’t very clear and I couldn’t reach Atmire today</li>
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<li>We want to do the <code>dc.type.output</code> move on CGSpace anyways, but we should wait as it might affect other external people!</li>
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</ul>
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<h2 id="2016-04-14:c88be15f5b2f07c85f7742556a955e47">2016-04-14</h2>
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<ul>
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<li>Communicate with Macaroni Bros again about <code>dc.type</code></li>
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<li>Help Sisay with some rsync and Linux stuff</li>
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<li>Notify CIAT people of metadata changes (I had forgotten them last week)</li>
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</ul>
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<h2 id="2016-04-15:c88be15f5b2f07c85f7742556a955e47">2016-04-15</h2>
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<ul>
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<li>DSpace Test had crashed, so I ran all system updates, rebooted, and re-deployed DSpace code</li>
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