Update notes for 2018-05-15
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@ -175,6 +175,7 @@ $ lein run /tmp/crps.csv id
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## 2018-05-14
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- Send a message to the OpenRefine mailing list about the bug with reconciling multi-value cells
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- Help Silvia Alonso get a list of all her publications since 2013 from Listings and Reports
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## 2018-05-15
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@ -200,3 +201,52 @@ return "blank"
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- More information and good examples here: https://programminghistorian.org/lessons/fetch-and-parse-data-with-openrefine
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- Finish looking at the 2,640 CIFOR records on DSpace Test ([10568/92904](https://dspacetest.cgiar.org/handle/10568/92904)), cleaning up authors and adding collection mappings
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- They can now be moved to CGSpace as far as I'm concerned, but I don't know if Sisay will do it or me
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- I was checking the CIFOR data for duplicates using Atmire's Metadata Quality Module (and found some duplicates actually), but then DSpace died...
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- I didn't see anything in the Tomcat, DSpace, or Solr logs, but I saw this in `dmest -T`:
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```
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[Tue May 15 12:10:01 2018] Out of memory: Kill process 3763 (java) score 706 or sacrifice child
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[Tue May 15 12:10:01 2018] Killed process 3763 (java) total-vm:14667688kB, anon-rss:5705268kB, file-rss:0kB, shmem-rss:0kB
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[Tue May 15 12:10:01 2018] oom_reaper: reaped process 3763 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
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```
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- So the Linux kernel killed Java...
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- Maria from Bioversity mailed to say she got an error while submitting an item on CGSpace:
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```
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Unable to load Submission Information, since WorkspaceID (ID:S96060) is not a valid in-process submission
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```
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- Looking in the DSpace log I see something related:
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```
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2018-05-15 12:35:30,858 INFO org.dspace.submit.step.CompleteStep @ m.garruccio@cgiar.org:session_id=8AC4499945F38B45EF7A1226E3042DAE:submission_complete:Completed submission with id=96060
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```
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- So I'm not sure...
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- I finally figured out how to get OpenRefine to reconcile values from Solr via [conciliator](https://github.com/codeforkjeff/conciliator):
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- The trick was to use a more appropriate Solr fieldType `text_en` instead of `text_general` so that more terms match, for example uppercase and lower case:
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```
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$ ./bin/solr start
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$ ./bin/solr create_core -c countries
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$ ./bin/post -c countries ~/src/git/DSpace/2018-05-10-countries.csv
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$ curl -X POST -H 'Content-type:application/json' --data-binary '{"add-field": {"name":"country", "type":"text_en", "multiValued":false, "stored":true}}' http://localhost:8983/solr/countries/schema
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```
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- It still doesn't catch simple mistakes like "ALBANI" or "AL BANIA" for "ALBANIA", and it doesn't return scores, so I have to select matches manually:
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- I should probably make a general copy field and set it to be the default search field, like DSpace's search core does (see schema.xml):
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```
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<defaultSearchField>search_text</defaultSearchField>
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...
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<copyField source="*" dest="search_text"/>
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```
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- Actually, I wonder how much of their schema I could just copy...
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- Apparently the default search field is the `df` parameter and you could technically just add it to the query string, so no need to bother with that in the schema now
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- I copied over the DSpace `search_text` field type from the DSpace Solr config (had to remove some properties so Solr would start) but it doesn't seem to be any better at matching than the `text_en` type
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- I think I need to focus on trying to return scores with conciliator
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@ -27,7 +27,7 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
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<meta property="article:published_time" content="2018-05-01T16:43:54+03:00"/>
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<meta property="article:modified_time" content="2018-05-13T18:30:25+03:00"/>
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<meta property="article:modified_time" content="2018-05-15T13:25:03+03:00"/>
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@ -65,9 +65,9 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
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"@type": "BlogPosting",
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"headline": "May, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-05/",
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"wordCount": "1441",
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"wordCount": "1811",
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"datePublished": "2018-05-01T16:43:54+03:00",
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"dateModified": "2018-05-13T18:30:25+03:00",
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"dateModified": "2018-05-15T13:25:03+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -340,6 +340,7 @@ Livestock and Fish
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<ul>
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<li>Send a message to the OpenRefine mailing list about the bug with reconciling multi-value cells</li>
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<li>Help Silvia Alonso get a list of all her publications since 2013 from Listings and Reports</li>
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</ul>
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<h2 id="2018-05-15">2018-05-15</h2>
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@ -368,6 +369,62 @@ return "blank"
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<li>More information and good examples here: <a href="https://programminghistorian.org/lessons/fetch-and-parse-data-with-openrefine">https://programminghistorian.org/lessons/fetch-and-parse-data-with-openrefine</a></li>
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<li>Finish looking at the 2,640 CIFOR records on DSpace Test (<a href="https://dspacetest.cgiar.org/handle/10568/92904"><sup>10568</sup>⁄<sub>92904</sub></a>), cleaning up authors and adding collection mappings</li>
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<li>They can now be moved to CGSpace as far as I’m concerned, but I don’t know if Sisay will do it or me</li>
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<li>I was checking the CIFOR data for duplicates using Atmire’s Metadata Quality Module (and found some duplicates actually), but then DSpace died…</li>
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<li>I didn’t see anything in the Tomcat, DSpace, or Solr logs, but I saw this in <code>dmest -T</code>:</li>
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</ul>
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<pre><code>[Tue May 15 12:10:01 2018] Out of memory: Kill process 3763 (java) score 706 or sacrifice child
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[Tue May 15 12:10:01 2018] Killed process 3763 (java) total-vm:14667688kB, anon-rss:5705268kB, file-rss:0kB, shmem-rss:0kB
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[Tue May 15 12:10:01 2018] oom_reaper: reaped process 3763 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
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</code></pre>
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<ul>
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<li>So the Linux kernel killed Java…</li>
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<li>Maria from Bioversity mailed to say she got an error while submitting an item on CGSpace:</li>
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</ul>
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<pre><code>Unable to load Submission Information, since WorkspaceID (ID:S96060) is not a valid in-process submission
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</code></pre>
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<ul>
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<li>Looking in the DSpace log I see something related:</li>
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</ul>
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<pre><code>2018-05-15 12:35:30,858 INFO org.dspace.submit.step.CompleteStep @ m.garruccio@cgiar.org:session_id=8AC4499945F38B45EF7A1226E3042DAE:submission_complete:Completed submission with id=96060
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</code></pre>
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<ul>
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<li>So I’m not sure…</li>
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<li>I finally figured out how to get OpenRefine to reconcile values from Solr via <a href="https://github.com/codeforkjeff/conciliator">conciliator</a>:</li>
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<li>The trick was to use a more appropriate Solr fieldType <code>text_en</code> instead of <code>text_general</code> so that more terms match, for example uppercase and lower case:</li>
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</ul>
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<pre><code>$ ./bin/solr start
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$ ./bin/solr create_core -c countries
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$ ./bin/post -c countries ~/src/git/DSpace/2018-05-10-countries.csv
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$ curl -X POST -H 'Content-type:application/json' --data-binary '{"add-field": {"name":"country", "type":"text_en", "multiValued":false, "stored":true}}' http://localhost:8983/solr/countries/schema
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</code></pre>
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<ul>
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<li>It still doesn’t catch simple mistakes like “ALBANI” or “AL BANIA” for “ALBANIA”, and it doesn’t return scores, so I have to select matches manually:</li>
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</ul>
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<p><img src="/cgspace-notes/2018/05/openrefine-solr-conciliator.png" alt="OpenRefine reconciling countries from local Solr" /></p>
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<ul>
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<li>I should probably make a general copy field and set it to be the default search field, like DSpace’s search core does (see schema.xml):</li>
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</ul>
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<pre><code><defaultSearchField>search_text</defaultSearchField>
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...
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<copyField source="*" dest="search_text"/>
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</code></pre>
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<ul>
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<li>Actually, I wonder how much of their schema I could just copy…</li>
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<li>Apparently the default search field is the <code>df</code> parameter and you could technically just add it to the query string, so no need to bother with that in the schema now</li>
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<li>I copied over the DSpace <code>search_text</code> field type from the DSpace Solr config (had to remove some properties so Solr would start) but it doesn’t seem to be any better at matching than the <code>text_en</code> type</li>
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<li>I think I need to focus on trying to return scores with conciliator</li>
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</ul>
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@ -4,7 +4,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2018-05/</loc>
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<lastmod>2018-05-13T18:30:25+03:00</lastmod>
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<lastmod>2018-05-15T13:25:03+03:00</lastmod>
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</url>
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<url>
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@ -164,7 +164,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2018-05-13T18:30:25+03:00</lastmod>
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<lastmod>2018-05-15T13:25:03+03:00</lastmod>
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<priority>0</priority>
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</url>
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@ -175,7 +175,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2018-05-13T18:30:25+03:00</lastmod>
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<lastmod>2018-05-15T13:25:03+03:00</lastmod>
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<priority>0</priority>
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</url>
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@ -187,13 +187,13 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
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<lastmod>2018-05-13T18:30:25+03:00</lastmod>
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<lastmod>2018-05-15T13:25:03+03:00</lastmod>
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
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<lastmod>2018-05-13T18:30:25+03:00</lastmod>
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<lastmod>2018-05-15T13:25:03+03:00</lastmod>
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<priority>0</priority>
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</url>
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