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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-12-02T10:43:00+03:00">Fri Dec 02, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-12-02">2016-12-02</h2>
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<ul>
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<li>CGSpace was down for five hours in the morning while I was sleeping</li>
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<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
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</ul>
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<pre tabindex="0"><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail="dc.title", transactionID="TX157907838689377964651674089851855413607")
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail="THUMBNAIL", transactionID="TX157907838689377964651674089851855413607")
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail="-1", transactionID="TX157907838689377964651674089851855413607")
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
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</code></pre><ul>
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<li>I see thousands of them in the logs for the last few months, so it’s not related to the DSpace 5.5 upgrade</li>
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<li>I’ve raised a ticket with Atmire to ask</li>
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<li>Another worrying error from dspace.log is:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2016-12/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-11/">November, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-11-01T09:21:00+03:00">Tue Nov 01, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-11-01">2016-11-01</h2>
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<ul>
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<li>Add <code>dc.type</code> to the output options for Atmire’s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
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</ul>
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<p><img src="/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type"></p>
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<a href='https://alanorth.github.io/cgspace-notes/2016-11/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-10/">October, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-10-03T15:53:00+03:00">Mon Oct 03, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-10-03">2016-10-03</h2>
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<ul>
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<li>Testing adding <a href="https://wiki.lyrasis.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
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<li>Need to test the following scenarios to see how author order is affected:
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<ul>
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<li>ORCIDs only</li>
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<li>ORCIDs plus normal authors</li>
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</ul>
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</li>
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<li>I exported a random item’s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
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</ul>
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<pre tabindex="0"><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-09/">September, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-09-01T15:53:00+03:00">Thu Sep 01, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-09-01">2016-09-01</h2>
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<ul>
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<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
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<li>Discuss how the migration of CGIAR’s Active Directory to a flat structure will break our LDAP groups in DSpace</li>
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<li>We had been using <code>DC=ILRI</code> to determine whether a user was ILRI or not</li>
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<li>It looks like we might be able to use OUs now, instead of DCs:</li>
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</ul>
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<pre tabindex="0"><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2016-09/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-08/">August, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-08-01T15:53:00+03:00">Mon Aug 01, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-08-01">2016-08-01</h2>
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<ul>
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<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
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<li>Play with upgrading Mirage 2 dependencies in <code>bower.json</code> because most are several versions of out date</li>
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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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<pre tabindex="0"><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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<a href='https://alanorth.github.io/cgspace-notes/2016-08/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-07/">July, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-07-01T10:53:00+03:00">Fri Jul 01, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-07-01">2016-07-01</h2>
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<ul>
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<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
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<li>I think this query should find and replace all authors that have “,” at the end of their names:</li>
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</ul>
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<pre tabindex="0"><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
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UPDATE 95
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dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
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text_value
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------------
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(0 rows)
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</code></pre><ul>
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<li>In this case the select query was showing 95 results before the update</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2016-07/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-06/">June, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-06-01T10:53:00+03:00">Wed Jun 01, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-06-01">2016-06-01</h2>
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<ul>
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<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
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<li>After reading the <a href="https://www.oclc.org/support/services/contentdm/help/server-admin-help/oai-support.en.html">ContentDM documentation</a> I found IFPRI’s OAI endpoint: <a href="http://ebrary.ifpri.org/oai/oai.php">http://ebrary.ifpri.org/oai/oai.php</a></li>
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<li>After reading the <a href="https://www.openarchives.org/OAI/openarchivesprotocol.html">OAI documentation</a> and testing with an <a href="http://validator.oaipmh.com/">OAI validator</a> I found out how to get their publications</li>
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<li>This is their publications set: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&from=2016-01-01&set=p15738coll2&metadataPrefix=oai_dc">http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&from=2016-01-01&set=p15738coll2&metadataPrefix=oai_dc</a></li>
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<li>You can see the others by using the OAI <code>ListSets</code> verb: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListSets">http://ebrary.ifpri.org/oai/oai.php?verb=ListSets</a></li>
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<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-05/">May, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-05-01T23:06:00+03:00">Sun May 01, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-05-01">2016-05-01</h2>
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<ul>
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<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
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<li>I have blocked access to the API now</li>
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<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
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</ul>
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<pre tabindex="0"><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
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3168
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2016-05/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-04/">April, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-04-04T11:06:00+03:00">Mon Apr 04, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-04-04">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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<a href='https://alanorth.github.io/cgspace-notes/2016-04/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-03/">March, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-03-02T16:50:00+03:00">Wed Mar 02, 2016</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-03-02">2016-03-02</h2>
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<ul>
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<li>Looking at issues with author authorities on CGSpace</li>
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<li>For some reason we still have the <code>index-lucene-update</code> cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module</li>
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<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
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</ul>
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