Add notes for 2020-09-17

content/posts/2020-09.md

@@ -251,4 +251,58 @@ $ ~/dspace/bin/dspace import -a -e y.arrr@cgiar.org -m /tmp/2020-09-15-cip-annua
 
 - Then I uploaded them to CGSpace
 
+## 2020-09-16
+
+- Looking further into Carlos Tejos's question about integrating LandVoc (the AGROVOC subset) into DSpace
+  - I see that you can actually get LandVoc concepts directly from AGROVOC's SPARQL, for example with [this query](http://agrovoc.uniroma2.it/sparql#query=PREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0APREFIX+skos%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23%3E%0A%0ASELECT+%3Fconcept%0AWHERE+%7B%0A++%3Fconcept+a+skos%3AConcept+%3B%0A+++++++++++skos%3AinScheme+%3Chttp%3A%2F%2Flandvoc.org%2Flandvoc%3E+.%0A%0A%7D+ORDER+BY+%3Fconcept&contentTypeConstruct=text%2Fturtle&contentTypeSelect=application%2Fsparql-results%2Bjson&endpoint=http%3A%2F%2Fagrovoc.uniroma2.it%2Fsparql&requestMethod=POST&tabTitle=Query&headers=%7B%7D&outputFormat=table)
+
+![AGROVOC LandVoc SPARQL](/cgspace-notes/2020/09/agrovoc-landvoc-sparql.png)
+
+- So maybe we can query AGROVOC directly using a similar method to [DSpace-CRIS's GettyAuthority](https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace-api/src/main/java/org/dspace/content/authority/TGNAuthority.java)
+- I wired up DSpace-CRIS's VIAFAuthority to see how authorities for auto suggested names get stored
+  - After submission you can see the item's VIAF identifier:
+
+![VIAF authority](/cgspace-notes/2020/09/viaf-authority.png)
+
+- And this identifier is the ID on VIAF, pretty cool!
+
+![VIAF entry for Charles Darwin](/cgspace-notes/2020/09/viaf-darwin.png)
+
+- I did a similar test with the Getty Thesaurus of Geographic Names (TGN) and it stores the concept URI in the authority:
+
+![TGNAuthority](/cgspace-notes/2020/09/tgn-concept-uri.png)
+
+- But the authority values are not exposed anywhere as metadata...
+  - I need to play with it a bit more I guess...
+- The nice thing is that the Getty example from DSpace-CRIS uses SPARQL as well, and the TGN authority extends it
+  - We could use a similar model for AGROVOC/LandVoc very easily
+
+## 2020-09-17
+
+- Maria from Bioveristy asked about the ORCID identifier for one of her colleagues that seems to have been removed from our list
+  - I re-added it to our controlled vocabulary and added the identifier to fifty-one of his existing items on CGSpace using my script:
+
+```
+$ cat 2020-09-17-add-bioversity-orcids.csv
+dc.contributor.author,cg.creator.id
+"Etten, Jacob van","Jacob van Etten: 0000-0001-7554-2558"
+"van Etten, Jacob","Jacob van Etten: 0000-0001-7554-2558"
+$ ./add-orcid-identifiers-csv.py -i 2020-09-17-add-bioversity-orcids.csv -db dspace -u dspace -p 'dom@in34sniper'
+```
+
+- I sent a follow-up message to Atmire to look into the two remaining issues with the DSpace 6 upgrade
+  - First is the fact that we have zero results in our Listings and Reports, for any search
+  - Second is the error we get during CSV imports
+- Help Natalia and Cathy from Bioversity-CIAT with their OpenSearch query on "trade offs" again
+  - They wanted to build a search query with multiple filters (type, crpsubject, status) and the general query "trade offs"
+  - I found a great [reference for DSpace's OpenSearch syntax](https://www.kiwi.fi/pages/viewpage.action?pageId=45782169) (albeit in Finnish, but the example URLs show the syntax clearly)
+  - We can use quotes and `AND` and `OR` and even group search parameters with parenthesis!
+  - So now I built a query for Natalia which uses these (showing without URL encoding so you can see the syntax):
+
+```
+https://cgspace.cgiar.org/open-search/discover?query=type:"Journal Article" AND status:"Open Access" AND crpsubject:"Water, Land and Ecosystems" AND "tradeoffs"&rpp=100
+```
+
+- I noticed that my `move-collections.sh` script didn't work on DSpace 6 because of the change from IDs to UUIDs, so I modified it to quote the collection `resource_id` parameters in the PostgreSQL query
+
 <!-- vim: set sw=2 ts=2: -->

docs/2020-09/index.html

@@ -55,7 +55,7 @@ I filed an issue on OpenRXV to make some minor edits to the admin UI: https://gi
   "@type": "BlogPosting",
   "headline": "September, 2020",
   "url": "https://alanorth.github.io/cgspace-notes/2020-09/",
-  "wordCount": "1911",
+  "wordCount": "2161",
   "datePublished": "2020-09-02T15:35:54+03:00",
   "dateModified": "2020-09-15T17:32:29+03:00",
   "author": {
@@ -464,6 +464,39 @@ Would fix 3 occurences of: SOUTHWEST ASIA
 </ul>
 </li>
 </ul>
+<h2 id="2020-09-17">2020-09-17</h2>
+<ul>
+<li>Maria from Bioveristy asked about the ORCID identifier for one of her colleagues that seems to have been removed from our list
+<ul>
+<li>I re-added it to our controlled vocabulary and added the identifier to fifty-one of his existing items on CGSpace using my script:</li>
+</ul>
+</li>
+</ul>
+<pre><code>$ cat 2020-09-17-add-bioversity-orcids.csv
+dc.contributor.author,cg.creator.id
+&quot;Etten, Jacob van&quot;,&quot;Jacob van Etten: 0000-0001-7554-2558&quot;
+&quot;van Etten, Jacob&quot;,&quot;Jacob van Etten: 0000-0001-7554-2558&quot;
+$ ./add-orcid-identifiers-csv.py -i 2020-09-17-add-bioversity-orcids.csv -db dspace -u dspace -p 'dom@in34sniper'
+</code></pre><ul>
+<li>I sent a follow-up message to Atmire to look into the two remaining issues with the DSpace 6 upgrade
+<ul>
+<li>First is the fact that we have zero results in our Listings and Reports, for any search</li>
+<li>Second is the error we get during CSV imports</li>
+</ul>
+</li>
+<li>Help Natalia and Cathy from Bioversity-CIAT with their OpenSearch query on &ldquo;trade offs&rdquo; again
+<ul>
+<li>They wanted to build a search query with multiple filters (type, crpsubject, status) and the general query &ldquo;trade offs&rdquo;</li>
+<li>I found a great <a href="https://www.kiwi.fi/pages/viewpage.action?pageId=45782169">reference for DSpace&rsquo;s OpenSearch syntax</a> (albeit in Finnish, but the example URLs show the syntax clearly)</li>
+<li>We can use quotes and <code>AND</code> and <code>OR</code> and even group search parameters with parenthesis!</li>
+<li>So now I built a query for Natalia which uses these (showing without URL encoding so you can see the syntax):</li>
+</ul>
+</li>
+</ul>
+<pre><code>https://cgspace.cgiar.org/open-search/discover?query=type:&quot;Journal Article&quot; AND status:&quot;Open Access&quot; AND crpsubject:&quot;Water, Land and Ecosystems&quot; AND &quot;tradeoffs&quot;&amp;rpp=100
+</code></pre><ul>
+<li>I noticed that my <code>move-collections.sh</code> script didn&rsquo;t work on DSpace 6 because of the change from IDs to UUIDs, so I modified it to quote the collection <code>resource_id</code> parameters in the PostgreSQL query</li>
+</ul>
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