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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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</time>
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<span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span>
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</header>
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<section>
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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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</ul>
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<h2 id="2016-04-18:c88be15f5b2f07c85f7742556a955e47">2016-04-18</h2>
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<ul>
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<li>Talk to CIAT people about their portal again</li>
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<li>Start looking more at the fields we want to delete</li>
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<li>The following metadata fields have 0 items using them, so we can just remove them from the registry and any references in XMLUI, input forms, etc:
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<ul>
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<li>dc.description.abstractother</li>
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<li>dc.whatwasknown</li>
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<li>dc.whatisnew</li>
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<li>dc.description.nationalpartners</li>
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<li>dc.peerreviewprocess</li>
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<li>cg.species.animal</li>
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</ul></li>
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<li>Deleted!</li>
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<li>The following fields have some items using them and I have to decide what to do with them (delete or move):
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<ul>
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<li>dc.icsubject.icrafsubject: 6 items, mostly in CPWF collections</li>
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<li>dc.type.journal: 11 items, mostly in ILRI collections</li>
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<li>dc.publicationcategory: 1 item, in CPWF</li>
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<li>dc.GRP: 2 items, CPWF</li>
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<li>dc.Species.animal: 6 items, in ILRI and AnGR</li>
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<li>cg.livestock.agegroup: 9 items, in ILRI collections</li>
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<li>cg.livestock.function: 20 items, mostly in EADD</li>
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</ul></li>
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<li>Test metadata migration on local instance again:</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 40885
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UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
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UPDATE 51330
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UPDATE metadatavalue SET metadata_field_id=208 WHERE metadata_field_id=82
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UPDATE 5986
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UPDATE metadatavalue SET metadata_field_id=210 WHERE metadata_field_id=88
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UPDATE 2456
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UPDATE metadatavalue SET metadata_field_id=215 WHERE metadata_field_id=106
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UPDATE 3872
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UPDATE metadatavalue SET metadata_field_id=217 WHERE metadata_field_id=108
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UPDATE 46075
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$ JAVA_OPTS="-Xms512m -Xmx512m -Dfile.encoding=UTF-8" ~/dspace/bin/dspace index-discovery -bf
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</code></pre>
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<ul>
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<li>CGSpace was down but I’m not sure why, this was in <code>catalina.out</code>:</li>
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</ul>
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<pre><code>Apr 18, 2016 7:32:26 PM com.sun.jersey.spi.container.ContainerResponse logException
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SEVERE: Mapped exception to response: 500 (Internal Server Error)
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javax.ws.rs.WebApplicationException
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at org.dspace.rest.Resource.processFinally(Resource.java:163)
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at org.dspace.rest.HandleResource.getObject(HandleResource.java:81)
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at sun.reflect.GeneratedMethodAccessor198.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 com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
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at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185)
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at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
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at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
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at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
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at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
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at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
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at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
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at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1511)
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at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1442)
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at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1391)
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at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1381)
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at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
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...
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</code></pre>
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<ul>
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<li>Everything else in the system looked normal (50GB disk space available, nothing weird in dmesg, etc)</li>
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<li>After restarting Tomcat a few more of these errors were logged but the application was up</li>
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</ul>
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<h2 id="2016-04-19:c88be15f5b2f07c85f7742556a955e47">2016-04-19</h2>
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<ul>
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<li>Get handles for items that are using a given metadata field, ie <code>dc.Species.animal</code> (105):</li>
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</ul>
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<pre><code># select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=105);
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handle
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-------------
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10568/10298
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10568/16413
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10568/16774
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10568/34487
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</code></pre>
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<ul>
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<li>Delete metadata values for <code>dc.GRP</code> and <code>dc.icsubject.icrafsubject</code>:</li>
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</ul>
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<pre><code># delete from metadatavalue where resource_type_id=2 and metadata_field_id=96;
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# delete from metadatavalue where resource_type_id=2 and metadata_field_id=83;
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</code></pre>
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<ul>
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<li>They are old ICRAF fields and we haven’t used them since 2011 or so</li>
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<li>Also delete them from the metadata registry</li>
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<li>CGSpace went down again, <code>dspace.log</code> had this:</li>
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</ul>
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<pre><code>2016-04-19 15:02:17,025 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
|
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
|
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</code></pre>
|
|
|
|
<ul>
|
|
<li>I restarted Tomcat and PostgreSQL and now it’s back up</li>
|
|
<li>I bet this is the same crash as yesterday, but I only saw the errors in <code>catalina.out</code></li>
|
|
<li>Looks to be related to this, from <code>dspace.log</code>:</li>
|
|
</ul>
|
|
|
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<pre><code>2016-04-19 15:16:34,670 ERROR org.dspace.rest.Resource @ Something get wrong. Aborting context in finally statement.
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|
</code></pre>
|
|
|
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<ul>
|
|
<li>We have 18,000 of these errors right now…</li>
|
|
<li>Delete a few more old metadata values: <code>dc.Species.animal</code>, <code>dc.type.journal</code>, and <code>dc.publicationcategory</code>:</li>
|
|
</ul>
|
|
|
|
<pre><code># delete from metadatavalue where resource_type_id=2 and metadata_field_id=105;
|
|
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=85;
|
|
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=95;
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>And then remove them from the metadata registry</li>
|
|
</ul>
|
|
|
|
<h2 id="2016-04-20:c88be15f5b2f07c85f7742556a955e47">2016-04-20</h2>
|
|
|
|
<ul>
|
|
<li>Re-deploy DSpace Test with the new subject and type fields, run all system updates, and reboot the server</li>
|
|
<li>Migrate fields and re-deploy CGSpace with the new subject and type fields, run all system updates, and reboot the server</li>
|
|
<li>Field migration went well:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ ./migrate-fields.sh
|
|
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
|
|
UPDATE 40909
|
|
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
|
|
UPDATE 51419
|
|
UPDATE metadatavalue SET metadata_field_id=208 WHERE metadata_field_id=82
|
|
UPDATE 5986
|
|
UPDATE metadatavalue SET metadata_field_id=210 WHERE metadata_field_id=88
|
|
UPDATE 2458
|
|
UPDATE metadatavalue SET metadata_field_id=215 WHERE metadata_field_id=106
|
|
UPDATE 3872
|
|
UPDATE metadatavalue SET metadata_field_id=217 WHERE metadata_field_id=108
|
|
UPDATE 46075
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Also, I migrated CGSpace to using the PGDG PostgreSQL repo as the infrastructure playbooks had been using it for a while and it seemed to be working well</li>
|
|
<li>Basically, this gives us the ability to use the latest upstream stable 9.3.x release (currently 9.3.12)</li>
|
|
<li>Looking into the REST API errors again, it looks like these started appearing a few days ago in the tens of thousands:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -c "Aborting context in finally statement" dspace.log.2016-04-20
|
|
21252
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I found a recent discussion on the DSpace mailing list and I’ve asked for advice there</li>
|
|
<li>Looks like this issue was noted and fixed in DSpace 5.5 (we’re on 5.1): <a href="https://jira.duraspace.org/browse/DS-2936">https://jira.duraspace.org/browse/DS-2936</a></li>
|
|
<li>I’ve sent a message to Atmire asking about compatibility with DSpace 5.5</li>
|
|
</ul>
|
|
|
|
<h2 id="2016-04-21:c88be15f5b2f07c85f7742556a955e47">2016-04-21</h2>
|
|
|
|
<ul>
|
|
<li>Fix a bunch of metadata consistency issues with IITA Journal Articles (Peer review, Formally published, messed up DOIs, etc)</li>
|
|
<li>Atmire responded with DSpace 5.5 compatible versions for their modules, so I’ll start testing those in a few weeks</li>
|
|
</ul>
|
|
|
|
<h2 id="2016-04-22:c88be15f5b2f07c85f7742556a955e47">2016-04-22</h2>
|
|
|
|
<ul>
|
|
<li>Import 95 records into <a href="https://cgspace.cgiar.org/handle/10568/42219">CTA’s Agrodok collection</a></li>
|
|
</ul>
|
|
|
|
<h2 id="2016-04-26:c88be15f5b2f07c85f7742556a955e47">2016-04-26</h2>
|
|
|
|
<ul>
|
|
<li>Test embargo during item upload</li>
|
|
<li>Seems to be working but the help text is misleading as to the date format</li>
|
|
<li>It turns out the <code>robots.txt</code> issue we thought we solved last month isn’t solved because you can’t use wildcards in URL patterns: <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li>
|
|
<li>Write some nginx rules to add <code>X-Robots-Tag</code> HTTP headers to the dynamic requests from <code>robots.txt</code> instead</li>
|
|
<li>A few URLs to test with:
|
|
|
|
<ul>
|
|
<li><a href="https://dspacetest.cgiar.org/handle/10568/440/browse?type=bioversity">https://dspacetest.cgiar.org/handle/10568/440/browse?type=bioversity</a></li>
|
|
<li><a href="https://dspacetest.cgiar.org/handle/10568/913/discover">https://dspacetest.cgiar.org/handle/10568/913/discover</a></li>
|
|
<li><a href="https://dspacetest.cgiar.org/handle/10568/1/search-filter?filtertype_0=country&filter_0=VIETNAM&filter_relational_operator_0=equals&field=country">https://dspacetest.cgiar.org/handle/10568/1/search-filter?filtertype_0=country&filter_0=VIETNAM&filter_relational_operator_0=equals&field=country</a></li>
|
|
</ul></li>
|
|
</ul>
|
|
|
|
<h2 id="2016-04-27:c88be15f5b2f07c85f7742556a955e47">2016-04-27</h2>
|
|
|
|
<ul>
|
|
<li>I woke up to ten or fifteen “up” and “down” emails from the monitoring website</li>
|
|
<li>Looks like the last one was “down” from about four hours ago</li>
|
|
<li>I think there must be something with this REST stuff:</li>
|
|
</ul>
|
|
|
|
<pre><code># grep -c "Aborting context in finally statement" dspace.log.2016-04-*
|
|
dspace.log.2016-04-01:0
|
|
dspace.log.2016-04-02:0
|
|
dspace.log.2016-04-03:0
|
|
dspace.log.2016-04-04:0
|
|
dspace.log.2016-04-05:0
|
|
dspace.log.2016-04-06:0
|
|
dspace.log.2016-04-07:0
|
|
dspace.log.2016-04-08:0
|
|
dspace.log.2016-04-09:0
|
|
dspace.log.2016-04-10:0
|
|
dspace.log.2016-04-11:0
|
|
dspace.log.2016-04-12:235
|
|
dspace.log.2016-04-13:44
|
|
dspace.log.2016-04-14:0
|
|
dspace.log.2016-04-15:35
|
|
dspace.log.2016-04-16:0
|
|
dspace.log.2016-04-17:0
|
|
dspace.log.2016-04-18:11942
|
|
dspace.log.2016-04-19:28496
|
|
dspace.log.2016-04-20:28474
|
|
dspace.log.2016-04-21:28654
|
|
dspace.log.2016-04-22:28763
|
|
dspace.log.2016-04-23:28773
|
|
dspace.log.2016-04-24:28775
|
|
dspace.log.2016-04-25:28626
|
|
dspace.log.2016-04-26:28655
|
|
dspace.log.2016-04-27:7271
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I restarted tomcat and it is back up</li>
|
|
</ul>
|
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<h1 class="author-name text-primary">Alan Orth</h1>
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