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Merge the Solr filterCache and XMLUI ISI journal changes to the 5_x-prod branch and deploy on CGSpace
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Run system updates on CGSpace (linode18) and reboot it
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2019-06-03
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Skype with Marie-Angélique and Abenet about CG Core v2
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<meta name="twitter:description" content="2019-06-02
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Merge the Solr filterCache and XMLUI ISI journal changes to the 5_x-prod branch and deploy on CGSpace
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Run system updates on CGSpace (linode18) and reboot it
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2019-06-03
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Skype with Marie-Angélique and Abenet about CG Core v2
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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/2019-06/">June, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-06-02T10:57:51+03:00">Sun Jun 02, 2019</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</header>
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<h2 id="2019-06-02">2019-06-02</h2>
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<ul>
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<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
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<li>Run system updates on CGSpace (linode18) and reboot it</li>
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</ul>
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<h2 id="2019-06-03">2019-06-03</h2>
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<ul>
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<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
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</ul>
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<ul>
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<li>Here is a list of proposed metadata migrations for CGSpace
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<ul>
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<li>dc.language.iso→DCTERMS.language (and switch to ISO 639-2 Alpha 3)</li>
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<li>dc.description.abstract→DCTERMS.abstract</li>
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<li>dc.identifier.citation→DCTERMS.bibliographicCitation</li>
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<li>dc.contributor.author→DCTERMS.creator (for people)</li>
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<li>dc.description.sponsorship→cg.contributor.donor (values from CrossRef or Grid.ac if possible)</li>
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<li>dc.rights→DCTERMS.license</li>
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<li>cg.identifier.status→DCTERMS.accessRights (values “open” or “restricted”)</li>
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<li>cg.creator.id→cg.creator.identifier?</li>
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<li>dc.relation.ispartofseries→DCTERMS.isPartOf</li>
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<li>cg.link.relation→DCTERMS.relation</li>
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</ul>
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</li>
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<li>Marie agreed that we need to adopt some controlled lists for our values, and pointed out that the MARLO team maintains a list of CRPs and Centers at <a href="https://clarisa.cgiar.org/">CLARISA</a>
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<ul>
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<li>There is an API there but it needs a password for access…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2019-06-04">2019-06-04</h2>
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<ul>
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<li>The MARLO team responded and said they will give us access to the CLARISA API</li>
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<li>Marie-Angélique <a href="https://github.com/AgriculturalSemantics/cg-core/pull/1">proposed</a> to integrate <code>dcterms.isPartOf</code>, <code>dcterms.abstract</code>, and <code>dcterms.bibliographicCitation</code> into the CG Core v2 schema
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<ul>
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<li>I told her I would attempt to integrate those and the others above into DSpace Test soon and report back</li>
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<li>We also need to discuss with the ILRI Data Portal, MEL/MELSpace, and users who consume the CGSpace API</li>
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</ul>
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</li>
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<li>Add Arabic language to input-forms.xml (<a href="https://github.com/ilri/DSpace/pull/427">#427</a>), as Bioversity is adding some Arabic items and noticed it missing</li>
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</ul>
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<h2 id="2019-06-05">2019-06-05</h2>
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<ul>
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<li>Send mail to CGSpace and MELSpace people to let them know about the proposed metadata field migrations after the discussion with Marie-Angélique</li>
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</ul>
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<h2 id="2019-06-07">2019-06-07</h2>
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<ul>
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<li>Thierry noticed that the CUA statistics were missing previous years again, and I see that the Solr admin UI has the following message:</li>
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</ul>
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<pre><code>statistics-2018: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
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</code></pre><ul>
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<li>I had to restart Tomcat a few times for all the stats cores to get loaded with no issue</li>
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</ul>
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<h2 id="2019-06-10">2019-06-10</h2>
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<ul>
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<li>Rename the AReS repository on GitHub to OpenRXV: <a href="https://github.com/ilri/OpenRXV">https://github.com/ilri/OpenRXV</a></li>
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<li>Create a new AReS repository: <a href="https://github.com/ilri/AReS">https://github.com/ilri/AReS</a></li>
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<li>Start looking at the 203 IITA records on DSpace Test from last month (<a href="https://dspacetest.cgiar.org/handle/10568/102032">IITA_May_16</a> aka “20194th.xls”) using OpenRefine
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<ul>
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<li>Trim leading, trailing, and consecutive whitespace on all columns, but I didn’t notice very many issues</li>
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<li>Validate affiliations against latest list of top 1500 terms using reconcile-csv, correcting and standardizing about twenty-seven</li>
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<li>Validate countries against latest list of countries using reconcile-csv, correcting three</li>
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<li>Convert all DOIs to “<a href="https://dx.doi.org">https://dx.doi.org</a>” format</li>
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<li>Normalize all <code>cg.identifier.url</code> Google book fields to “books.google.com”</li>
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<li>Correct some inconsistencies in IITA subjects</li>
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<li>Correct two incorrect “Peer Review” in <code>dc.description.version</code></li>
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<li>About fifteen items have incorrect ISBNs (looks like an Excel error because the values look like scientific numbers)</li>
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<li>Delete one blank item</li>
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<li>I managed to get to subjects, so I’ll continue from there when I start working next</li>
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</ul>
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</li>
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<li>Generate a new list of countries from the database for use with reconcile-csv
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<ul>
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<li>After dumping, use csvcut to add line numbers, then change the csv header to match those you use in reconcile-csv, for example <code>id</code> and <code>name</code>:</li>
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</ul>
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</li>
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</ul>
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<pre><code>dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 228 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC) to /tmp/countries.csv WITH CSV HEADER
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COPY 192
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$ csvcut -l -c 0 /tmp/countries.csv > 2019-06-10-countries.csv
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</code></pre><ul>
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<li>Get a list of all the unique AGROVOC subject terms in IITA’s data and export it to a text file so I can validate them with my <code>agrovoc-lookup.py</code> script:</li>
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</ul>
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<pre><code>$ csvcut -c dc.subject ~/Downloads/2019-06-10-IITA-20194th-Round-2.csv| sed 's/||/\n/g' | grep -v dc.subject | sort -u > iita-agrovoc.txt
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$ ./agrovoc-lookup.py -i iita-agrovoc.txt -om iita-agrovoc-matches.txt -or iita-agrovoc-rejects.txt
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$ wc -l iita-agrovoc*
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402 iita-agrovoc-matches.txt
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29 iita-agrovoc-rejects.txt
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431 iita-agrovoc.txt
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</code></pre><ul>
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<li>Combine these IITA matches with the subjects I matched a few months ago:</li>
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</ul>
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<pre><code>$ csvcut -c name 2019-03-18-subjects-matched.csv | grep -v name | cat - iita-agrovoc-matches.txt | sort -u > 2019-06-10-subjects-matched.txt
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</code></pre><ul>
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<li>Then make a new list to use with reconcile-csv by adding line numbers with csvcut and changing the line number header to <code>id</code>:</li>
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</ul>
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<pre><code>$ csvcut -c name -l 2019-06-10-subjects-matched.txt | sed 's/line_number/id/' > 2019-06-10-subjects-matched.csv
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</code></pre><h2 id="2019-06-20">2019-06-20</h2>
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<ul>
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<li>Share some feedback about AReS v2 with the colleagues and encourage them to do the same</li>
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</ul>
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<h2 id="2019-06-23">2019-06-23</h2>
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<ul>
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<li>Continue work on reviewing CG Core v2 standard and its implications to CGSpace an DSpace platforms in general
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<ul>
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<li>Update my <a href="https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409">list of fields to migrate</a></li>
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<li>Submit an <a href="https://github.com/AgriculturalSemantics/cg-core/issues/2">issue with my feedback to the CG Core project</a></li>
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</ul>
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</li>
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<li>Update my local PostgreSQL container:</li>
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</ul>
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<pre><code>$ podman pull docker.io/library/postgres:9.6-alpine
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$ podman rm dspacedb
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$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
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</code></pre><h2 id="2019-06-25">2019-06-25</h2>
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<ul>
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<li>Normalize <code>text_lang</code> values for metadata on DSpace Test and CGSpace:</li>
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</ul>
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<pre><code>dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('ethnob', 'en', '*', 'E.', '');
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UPDATE 1551
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dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IS NULL;
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UPDATE 2070
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dspace=# UPDATE metadatavalue SET text_lang='es_ES' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('es', 'spa');
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UPDATE 2
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</code></pre><ul>
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<li>Upload 202 IITA records from earlier this month (20194th.xls) to CGSpace</li>
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<li>Communicate with Bioversity contractor in charge of their migration from Typo3 to CGSpace</li>
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</ul>
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<h2 id="2019-06-28">2019-06-28</h2>
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<ul>
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<li>Start looking at the fifty-seven AfricaRice records sent by Ibnou earlier this month
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<ul>
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<li>First, I see there are several items with type “Book” and “Book Chapter” should go in an “AfricaRice books and book chapters” collection, but none exists in the AfricaRice community</li>
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<li>Trim and collapse consecutive whitespace on author, affiliation, authorship types, title, subjects, doi, issn, source, citation, country, sponsors</li>
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<li>Standardize and correct affiliations like “Africa Rice Cente” and “Africa Rice Centre”, including syntax errors with multi-value separators</li>
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<li>Lots of variation in affiliations, for example:
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<ul>
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<li>Université Abomey-Calavi</li>
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<li>Université d’Abomey</li>
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<li>Université d’Abomey Calavi</li>
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<li>Université d’Abomey-Calavi</li>
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<li>University of Abomey-Calavi</li>
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</ul>
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</li>
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<li>Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:
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<ul>
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<li><code>$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id</code></li>
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<li>I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colume and populate it using this GREL: <code>if(cell.recon.matched, cell.recon.match.name, value)</code></li>
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</ul>
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</li>
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<li>Replace smart quotes with standard ASCII ones</li>
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<li>Fix typos in authoriship types</li>
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<li>Validate and normalize subjects against our 2019-06 list using reconcile-csv and OpenRefine:
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<ul>
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<li><code>$ lein run ~/src/git/DSpace/2019-06-10-subjects-matched.csv name id</code></li>
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<li>Also add about 30 new AGROVOC subjects to our list that I verified manually</li>
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</ul>
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</li>
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<li>There is one duplicate, both have the same DOI: <a href="https://doi.org/10.1016/j.agwat.2018.06.018">https://doi.org/10.1016/j.agwat.2018.06.018</a></li>
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<li>Fix four ISBNs that were in the ISSN field</li>
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</ul>
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</li>
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</ul>
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<h2 id="2019-06-30">2019-06-30</h2>
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<ul>
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<li>Upload fifty-seven AfricaRice records to <a href="https://dspacetest.cgiar.org/handle/10568/102274">DSpace Test</a>
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<ul>
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<li>I created the SAF bundler with SAFBuilder and then imported via the CLI:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ dspace import -a -e me@cgiar.org -m 2019-06-30-AfricaRice-11to73.map -s /tmp/2019-06-30-AfricaRice-11to73
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</code></pre><ul>
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<li>I sent feedback about a few missing PDFs and one duplicate to Ibnou to check</li>
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<li>Run all system updates on DSpace Test (linode19) and reboot it</li>
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</ul>
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<li><a href="/cgspace-notes/2020-05/">May, 2020</a></li>
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<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
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<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
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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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