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<meta property="og:title" content="June, 2016" />
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<meta property="og:description" content="2016-06-01
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Experimenting with IFPRI OAI (we want to harvest their publications)
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After reading the ContentDM documentation I found IFPRI’s OAI endpoint: http://ebrary.ifpri.org/oai/oai.php
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After reading the OAI documentation and testing with an OAI validator I found out how to get their publications
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This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&from=2016-01-01&set=p15738coll2&metadataPrefix=oai_dc
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You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
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Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
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" />
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<meta name="twitter:title" content="June, 2016"/>
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<meta name="twitter:description" content="2016-06-01
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Experimenting with IFPRI OAI (we want to harvest their publications)
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After reading the ContentDM documentation I found IFPRI’s OAI endpoint: http://ebrary.ifpri.org/oai/oai.php
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After reading the OAI documentation and testing with an OAI validator I found out how to get their publications
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This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&from=2016-01-01&set=p15738coll2&metadataPrefix=oai_dc
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You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
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Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
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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/2016-06/">June, 2016</a></h2>
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<time datetime="2016-06-01T10:53:00+03:00">Wed Jun 01, 2016</time>
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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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<pre tabindex="0"><code>dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
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UPDATE 497
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dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
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UPDATE 14
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</code></pre><ul>
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<li>Fix a few minor miscellaneous issues in <code>dspace.cfg</code> (<a href="https://github.com/ilri/DSpace/pull/227">#227</a>)</li>
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</ul>
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<h2 id="2016-06-02">2016-06-02</h2>
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<ul>
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<li>Testing the configuration and theme changes for the upcoming metadata migration and I found some issues with <code>cg.coverage.admin-unit</code></li>
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<li>Seems that the Browse configuration in <code>dspace.cfg</code> can’t handle the ‘-’ in the field name:</li>
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</ul>
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<pre tabindex="0"><code>webui.browse.index.12 = subregion:metadata:cg.coverage.admin-unit:text
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</code></pre><ul>
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<li>But actually, I think since DSpace 4 or 5 (we are 5.1) the Browse indexes come from Discovery (defined in discovery.xml) so this is really just a parsing error</li>
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<li>I’ve sent a message to the DSpace mailing list to ask about the Browse index definition</li>
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<li>A user was having problems with submission and from the stacktrace it looks like a Sherpa/Romeo issue</li>
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<li>I found a thread on the mailing list talking about it and there is bug report and a patch: <a href="https://jira.duraspace.org/browse/DS-2740">https://jira.duraspace.org/browse/DS-2740</a></li>
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<li>The patch applies successfully on DSpace 5.1 so I will try it later</li>
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</ul>
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<h2 id="2016-06-03">2016-06-03</h2>
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<ul>
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<li>Investigating the CCAFS authority issue, I exported the metadata for the Videos collection</li>
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<li>The top two authors are:</li>
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</ul>
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<pre tabindex="0"><code>CGIAR Research Program on Climate Change, Agriculture and Food Security::acd00765-02f1-4b5b-92fa-bfa3877229ce::500
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CGIAR Research Program on Climate Change, Agriculture and Food Security::acd00765-02f1-4b5b-92fa-bfa3877229ce::600
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</code></pre><ul>
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<li>So the only difference is the “confidence”</li>
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<li>Ok, well THAT is interesting:</li>
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</ul>
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<pre tabindex="0"><code>dspacetest=# select text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like '%Orth, %';
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text_value | authority | confidence
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------------+--------------------------------------+------------
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Orth, A. | ab606e3a-2b04-4c7d-9423-14beccf54257 | -1
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Orth, A. | ab606e3a-2b04-4c7d-9423-14beccf54257 | -1
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Orth, A. | ab606e3a-2b04-4c7d-9423-14beccf54257 | -1
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Orth, Alan | | -1
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Orth, Alan | | -1
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Orth, Alan | | -1
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Orth, Alan | | -1
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Orth, A. | 05c2c622-d252-4efb-b9ed-95a07d3adf11 | -1
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Orth, A. | 05c2c622-d252-4efb-b9ed-95a07d3adf11 | -1
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Orth, A. | ab606e3a-2b04-4c7d-9423-14beccf54257 | -1
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Orth, A. | ab606e3a-2b04-4c7d-9423-14beccf54257 | -1
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Orth, Alan | ad281dbf-ef81-4007-96c3-a7f5d2eaa6d9 | 600
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Orth, Alan | ad281dbf-ef81-4007-96c3-a7f5d2eaa6d9 | 600
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(13 rows)
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</code></pre><ul>
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<li>And now an actually relevent example:</li>
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</ul>
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<pre tabindex="0"><code>dspacetest=# select count(*) from metadatavalue where metadata_field_id=3 and text_value like 'CGIAR Research Program on Climate Change, Agriculture and Food Security' and confidence = 500;
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count
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-------
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707
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(1 row)
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dspacetest=# select count(*) from metadatavalue where metadata_field_id=3 and text_value like 'CGIAR Research Program on Climate Change, Agriculture and Food Security' and confidence != 500;
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count
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-------
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253
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(1 row)
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</code></pre><ul>
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<li>Trying something experimental:</li>
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</ul>
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<pre tabindex="0"><code>dspacetest=# update metadatavalue set confidence=500 where metadata_field_id=3 and text_value like 'CGIAR Research Program on Climate Change, Agriculture and Food Security';
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UPDATE 960
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</code></pre><ul>
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<li>And then re-indexing authority and Discovery…?</li>
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<li>After Discovery reindex the CCAFS authors are all together in the Authors sidebar facet</li>
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<li>The docs for the ORCiD and Authority stuff for DSpace 5 mention changing the browse indexes to use the Authority as well:</li>
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</ul>
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<pre tabindex="0"><code>webui.browse.index.2 = author:metadataAuthority:dc.contributor.author:authority
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</code></pre><ul>
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<li>That would only be for the “Browse by” function… so we’ll have to see what effect that has later</li>
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</ul>
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<h2 id="2016-06-04">2016-06-04</h2>
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<ul>
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<li>Re-sync DSpace Test with CGSpace and perform test of metadata migration again</li>
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<li>Run phase two of metadata migrations on CGSpace (see the <a href="https://gist.github.com/alanorth/1a730bec5ac9457a8fb0e3e72c98d09c">migration notes</a>)</li>
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<li>Run all system updates and reboot CGSpace server</li>
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</ul>
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<h2 id="2016-06-07">2016-06-07</h2>
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<ul>
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<li>Figured out how to export a list of the unique values from a metadata field ordered by count:</li>
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</ul>
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<pre tabindex="0"><code>dspacetest=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=29 group by text_value order by count desc) to /tmp/sponsorship.csv with csv;
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</code></pre><ul>
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<li>
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<p>Identified the next round of fields to migrate:</p>
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<ul>
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<li>dc.title.jtitle → dc.source</li>
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<li>dc.crsubject.crpsubject → cg.contributor.crp</li>
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<li>dc.contributor.affiliation → cg.contributor.affiliation</li>
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<li>dc.Species → cg.species</li>
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<li>dc.contributor.corporate → dc.contributor</li>
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<li>dc.identifier.url → cg.identifier.url</li>
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<li>dc.identifier.doi → cg.identifier.doi</li>
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<li>dc.identifier.googleurl → cg.identifier.googleurl</li>
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<li>dc.identifier.dataurl → cg.identifier.dataurl</li>
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</ul>
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</li>
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<li>
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<p>Discuss pulling data from IFPRI’s ContentDM with Ryan Miller</p>
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</li>
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<li>
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<p>Looks like OAI is kinda obtuse for this, and if we use ContentDM’s API we’ll be able to access their internal field names (rather than trying to figure out how they stuffed them into various, repeated Dublin Core fields)</p>
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</li>
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</ul>
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<h2 id="2016-06-08">2016-06-08</h2>
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<ul>
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<li>Discuss controlled vocabularies for ~28 fields</li>
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<li>Looks like this is all we need: <a href="https://wiki.lyrasis.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ConfiguringControlledVocabularies">https://wiki.lyrasis.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ConfiguringControlledVocabularies</a></li>
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<li>I wrote an XPath expression to extract the ILRI subjects from <code>input-forms.xml</code> (from the xmlstarlet package):</li>
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</ul>
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<pre tabindex="0"><code>$ xml sel -t -m '//value-pairs[@value-pairs-name="ilrisubject"]/pair/displayed-value/text()' -c '.' -n dspace/config/input-forms.xml
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</code></pre><ul>
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<li>Write to Atmire about the use of <code>atmire.orcid.id</code> to see if we can change it</li>
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<li>Seems to be a virtual field that is queried from the authority cache… hmm</li>
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<li>In other news, I found out that the About page that we haven’t been using lives in <code>dspace/config/about.xml</code>, so now we can update the text</li>
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<li>File bug about <code>closed="true"</code> attribute of controlled vocabularies not working: <a href="https://jira.duraspace.org/browse/DS-3238">https://jira.duraspace.org/browse/DS-3238</a></li>
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</ul>
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<h2 id="2016-06-09">2016-06-09</h2>
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<ul>
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<li>Atmire explained that the <code>atmire.orcid.id</code> field doesn’t exist in the schema, as it actually comes from the authority cache during XMLUI run time</li>
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<li>This means we don’t see it when harvesting via OAI or REST, for example</li>
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<li>They opened a feature ticket on the DSpace tracker to ask for support of this: <a href="https://jira.duraspace.org/browse/DS-3239">https://jira.duraspace.org/browse/DS-3239</a></li>
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</ul>
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<h2 id="2016-06-10">2016-06-10</h2>
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<ul>
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<li>Investigating authority confidences</li>
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<li>It looks like the values are documented in <code>Choices.java</code></li>
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<li>Experiment with setting all 960 CCAFS author values to be 500:</li>
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</ul>
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<pre tabindex="0"><code>dspacetest=# SELECT authority, confidence FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=3 AND text_value = 'CGIAR Research Program on Climate Change, Agriculture and Food Security';
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dspacetest=# UPDATE metadatavalue set confidence = 500 where resource_type_id=2 AND metadata_field_id=3 AND text_value = 'CGIAR Research Program on Climate Change, Agriculture and Food Security';
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UPDATE 960
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</code></pre><ul>
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<li>After the database edit, I did a full Discovery re-index</li>
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<li>And now there are exactly 960 items in the authors facet for ‘CGIAR Research Program on Climate Change, Agriculture and Food Security’</li>
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<li>Now I ran the same on CGSpace</li>
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<li>Merge controlled vocabulary functionality for animal breeds to <code>5_x-prod</code> (<a href="https://github.com/ilri/DSpace/pull/236">#236</a>)</li>
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<li>Write python script to update metadata values in batch via PostgreSQL: <a href="https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897">fix-metadata-values.py</a></li>
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<li>We need to use this to correct some pretty ugly values in fields like <code>dc.description.sponsorship</code></li>
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<li>Merge item display tweaks from earlier this week (<a href="https://github.com/ilri/DSpace/pull/231">#231</a>)</li>
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<li>Merge controlled vocabulary functionality for subregions (<a href="https://github.com/ilri/DSpace/pull/238">#238</a>)</li>
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</ul>
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<h2 id="2016-06-11">2016-06-11</h2>
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<ul>
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<li>Merge controlled vocabulary for sponsorship field (<a href="https://github.com/ilri/DSpace/pull/239">#239</a>)</li>
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<li>Fix character encoding issues for animal breed lookup that I merged yesterday</li>
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</ul>
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<h2 id="2016-06-17">2016-06-17</h2>
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<ul>
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<li>Linode has free RAM upgrades for their 13th birthday so I migrated DSpace Test (4→8GB of RAM)</li>
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</ul>
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<h2 id="2016-06-18">2016-06-18</h2>
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<ul>
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<li>
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<p>Clean up titles and hints in <code>input-forms.xml</code> to use title/sentence case and a few more consistency things (<a href="https://github.com/ilri/DSpace/pull/241">#241</a>)</p>
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</li>
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<li>
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<p>The final list of fields to migrate in the third phase of metadata migrations is:</p>
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<ul>
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<li>dc.title.jtitle → dc.source</li>
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<li>dc.crsubject.crpsubject → cg.contributor.crp</li>
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<li>dc.contributor.affiliation → cg.contributor.affiliation</li>
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<li>dc.srplace.subregion → cg.coverage.subregion</li>
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<li>dc.Species → cg.species</li>
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<li>dc.contributor.corporate → dc.contributor</li>
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<li>dc.identifier.url → cg.identifier.url</li>
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<li>dc.identifier.doi → cg.identifier.doi</li>
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<li>dc.identifier.googleurl → cg.identifier.googleurl</li>
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<li>dc.identifier.dataurl → cg.identifier.dataurl</li>
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</ul>
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</li>
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<li>
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<p>Interesting “Sunburst” visualization on a Digital Commons page: <a href="http://www.repository.law.indiana.edu/sunburst.html">http://www.repository.law.indiana.edu/sunburst.html</a></p>
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</li>
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<li>
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<p>Final testing on metadata fix/delete for <code>dc.description.sponsorship</code> cleanup</p>
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</li>
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<li>
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<p>Need to run <code>fix-metadata-values.py</code> and then <code>fix-metadata-values.py</code></p>
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</li>
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</ul>
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<h2 id="2016-06-20">2016-06-20</h2>
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<ul>
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<li>CGSpace’s HTTPS certificate expired last night and I didn’t notice, had to renew:</li>
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</ul>
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<pre tabindex="0"><code># /opt/letsencrypt/letsencrypt-auto renew --standalone --pre-hook "/usr/bin/service nginx stop" --post-hook "/usr/bin/service nginx start"
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|
</code></pre><ul>
|
|
<li>I really need to fix that cron job…</li>
|
|
</ul>
|
|
<h2 id="2016-06-24">2016-06-24</h2>
|
|
<ul>
|
|
<li>Run the replacements/deletes for <code>dc.description.sponsorship</code> (investors) on CGSpace:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i investors-not-blank-not-delete-85.csv -f dc.description.sponsorship -t 'correct investor' -m 29 -d cgspace -p 'fuuu' -u cgspace
|
|
$ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.sponsorship -m 29 -d cgspace -p 'fuuu' -u cgspace
|
|
</code></pre><ul>
|
|
<li>The scripts for this are here:
|
|
<ul>
|
|
<li><a href="https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897">fix-metadata-values.py</a></li>
|
|
<li><a href="https://gist.github.com/alanorth/bd7d58c947f686401a2b1fadc78736be">delete-metadata-values.py</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Add new sponsors to controlled vocabulary (<a href="https://github.com/ilri/DSpace/pull/244">#244</a>)</li>
|
|
<li>Refine submission form labels and hints</li>
|
|
</ul>
|
|
<h2 id="2016-06-28">2016-06-28</h2>
|
|
<ul>
|
|
<li>Testing the cleanup of <code>dc.contributor.corporate</code> with 13 deletions and 121 replacements</li>
|
|
<li>There are still ~97 fields that weren’t indicated to do anything</li>
|
|
<li>After the above deletions and replacements I regenerated a CSV and sent it to Peter <em>et al</em> to have a look</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>dspacetest=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=126 group by text_value order by count desc) to /tmp/contributors-june28.csv with csv;
|
|
</code></pre><ul>
|
|
<li>Re-evaluate <code>dc.contributor.corporate</code> and it seems we will move it to <code>dc.contributor.author</code> as this is more in line with how editors are actually using it</li>
|
|
</ul>
|
|
<h2 id="2016-06-29">2016-06-29</h2>
|
|
<ul>
|
|
<li>Test run of <code>migrate-fields.sh</code> with the following re-mappings:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>72 55 #dc.source
|
|
86 230 #cg.contributor.crp
|
|
91 211 #cg.contributor.affiliation
|
|
94 212 #cg.species
|
|
107 231 #cg.coverage.subregion
|
|
126 3 #dc.contributor.author
|
|
73 219 #cg.identifier.url
|
|
74 220 #cg.identifier.doi
|
|
79 222 #cg.identifier.googleurl
|
|
89 223 #cg.identifier.dataurl
|
|
</code></pre><ul>
|
|
<li>Run all cleanups and deletions of <code>dc.contributor.corporate</code> on CGSpace:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i Corporate-Authors-Fix-121.csv -f dc.contributor.corporate -t 'Correct style' -m 126 -d cgspace -u cgspace -p 'fuuu'
|
|
$ ./fix-metadata-values.py -i Corporate-Authors-Fix-PB.csv -f dc.contributor.corporate -t 'should be' -m 126 -d cgspace -u cgspace -p 'fuuu'
|
|
$ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-Delete-13.csv -m 126 -u cgspace -d cgspace -p 'fuuu'
|
|
</code></pre><ul>
|
|
<li>Re-deploy CGSpace and DSpace Test with latest June changes</li>
|
|
<li>Now the sharing and Altmetric bits are more prominent:</li>
|
|
</ul>
|
|
<p><img src="/cgspace-notes/2016/06/xmlui-altmetric-sharing.png" alt="DSpace 5.1 XMLUI With Altmetric Badge"></p>
|
|
<ul>
|
|
<li>Run all system updates on the servers and reboot</li>
|
|
<li>Start working on config changes for phase three of the metadata migrations</li>
|
|
</ul>
|
|
<h2 id="2016-06-30">2016-06-30</h2>
|
|
<ul>
|
|
<li>Wow, there are 95 authors in the database who have ‘,’ at the end of their name:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code># select text_value from metadatavalue where metadata_field_id=3 and text_value like '%,';
|
|
</code></pre><ul>
|
|
<li>We need to use something like this to fix them, need to write a proper regex later:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code># update metadatavalue set text_value = regexp_replace(text_value, '(Poole, J),', '\1') where metadata_field_id=3 and text_value = 'Poole, J,';
|
|
</code></pre>
|
|
|
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</article>
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
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<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
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<li><a href="/cgspace-notes/2024-02/">February, 2024</a></li>
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<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
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<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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|
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
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|
|
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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