Add notes for 2018-07-03

content/posts/2018-07.md

@@ -53,4 +53,46 @@ $ dspace database migrate ignored
 - Discuss AgriKnowledge including our Handle identifier on their harvested items from CGSpace
 - They seem to be only interested in Gates-funded outputs, for example: https://www.agriknowledge.org/files/tm70mv21t
 
+## 2018-07-03
+
+- Finally finish with the CIFOR Archive records (a total of 2448):
+  - I mapped the 50 items that were duplicates from elsewhere in CGSpace into [CIFOR Archive](https://cgspace.cgiar.org/handle/10568/16702)
+  - I did one last check of the remaining 2398 items and found eight who have a `cg.identifier.doi` that links to some URL other than a DOI so I moved those to `cg.identifier.url` and `cg.identifier.googleurl` as appropriate
+  - Also, thirteen items had a DOI in their citation, but did not have a `cg.identifier.doi` field, so I added those
+  - Then I imported those 2398 items in two batches (to deal with memory issues):
+
+```
+$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
+$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive.csv
+$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive2.csv
+```
+
+- I noticed there are many items that use HTTP instead of HTTPS for their Google Books URL, and some missing HTTP entirely:
+
+```
+dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
+ count
+-------
+   785
+dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
+ count
+-------
+     4
+```
+
+- I think I should fix that as well as some other garbage values like "test" and "dspace.ilri.org" etc:
+
+```
+dspace=# begin;
+dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
+UPDATE 785
+dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
+UPDATE 4
+dspace=# update metadatavalue set text_value='https://books.google.com/books?id=meF1CLdPSF4C' where resource_type_id=2 and metadata_field_id=222 and text_value='meF1CLdPSF4C';
+UPDATE 1
+dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=222 and metadata_value_id in (2299312, 10684, 10700, 996403);
+DELETE 4
+dspace=# commit;
+```
+
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docs/2015-11/index.html

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docs/2015-12/index.html

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docs/2016-01/index.html

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docs/2016-02/index.html

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docs/2016-03/index.html

@@ -45,7 +45,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
 
 
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docs/2016-04/index.html

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docs/2016-05/index.html

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docs/2016-06/index.html

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docs/2016-07/index.html

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docs/2016-08/index.html

@@ -61,7 +61,7 @@ $ git rebase -i dspace-5.5
 
 
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docs/2016-09/index.html

@@ -53,7 +53,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=or
 
 
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docs/2016-10/index.html

@@ -61,7 +61,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id
 
 
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docs/2016-11/index.html

@@ -45,7 +45,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module
 
 
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docs/2016-12/index.html

@@ -69,7 +69,7 @@ Another worrying error from dspace.log is:
 
 
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docs/2017-01/index.html

@@ -45,7 +45,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
 
 
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docs/2017-02/index.html

@@ -73,7 +73,7 @@ Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name
 
 
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docs/2017-03/index.html

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docs/2017-04/index.html

@@ -63,7 +63,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Th
 
 
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+<meta name="generator" content="Hugo 0.42.2" />
 
 
     

docs/2017-05/index.html

@@ -29,7 +29,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2017"/>
 <meta name="twitter:description" content="2017-05-01  ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items:  https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683   2017-05-02  Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request  2017-05-04  Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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docs/2017-06/index.html

@@ -29,7 +29,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="June, 2017"/>
 <meta name="twitter:description" content="2017-06-01  After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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docs/2017-07/index.html

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docs/2017-08/index.html

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docs/2017-09/index.html

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docs/2017-10/index.html

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docs/2017-11/index.html

@@ -77,7 +77,7 @@ COPY 54701
 
 
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docs/2017-12/index.html

@@ -47,7 +47,7 @@ The list of connections to XMLUI and REST API for today:
 
 
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docs/2018-01/index.html

@@ -185,7 +185,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
 
 
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docs/2018-02/index.html

@@ -47,7 +47,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-pl
 
 
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docs/2018-03/index.html

@@ -41,7 +41,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
 
 
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docs/2018-04/index.html

@@ -43,7 +43,7 @@ Catalina logs at least show some memory errors yesterday:
 
 
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docs/2018-05/index.html

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docs/2018-06/index.html

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docs/2018-07/index.html

@@ -30,7 +30,7 @@ There is insufficient memory for the Java Runtime Environment to continue.
 
 <meta property="article:published_time" content="2018-07-01T12:56:54&#43;03:00"/>
 
-<meta property="article:modified_time" content="2018-07-01T18:05:01&#43;03:00"/>
+<meta property="article:modified_time" content="2018-07-02T17:33:38&#43;03:00"/>
 
 
 
@@ -61,7 +61,7 @@ There is insufficient memory for the Java Runtime Environment to continue.
 
 
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@@ -71,9 +71,9 @@ There is insufficient memory for the Java Runtime Environment to continue.
   "@type": "BlogPosting",
   "headline": "July, 2018",
   "url": "https://alanorth.github.io/cgspace-notes/2018-07/",
-  "wordCount": "210",
+  "wordCount": "469",
   "datePublished": "2018-07-01T12:56:54&#43;03:00",
-  "dateModified": "2018-07-01T18:05:01&#43;03:00",
+  "dateModified": "2018-07-02T17:33:38&#43;03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -195,6 +195,54 @@ $ dspace database migrate ignored
 <li>They seem to be only interested in Gates-funded outputs, for example: <a href="https://www.agriknowledge.org/files/tm70mv21t">https://www.agriknowledge.org/files/tm70mv21t</a></li>
 </ul>
 
+<h2 id="2018-07-03">2018-07-03</h2>
+
+<ul>
+<li>Finally finish with the CIFOR Archive records (a total of 2448):
+
+<ul>
+<li>I mapped the 50 items that were duplicates from elsewhere in CGSpace into <a href="https://cgspace.cgiar.org/handle/10568/16702">CIFOR Archive</a></li>
+<li>I did one last check of the remaining 2398 items and found eight who have a <code>cg.identifier.doi</code> that links to some URL other than a DOI so I moved those to <code>cg.identifier.url</code> and <code>cg.identifier.googleurl</code> as appropriate</li>
+<li>Also, thirteen items had a DOI in their citation, but did not have a <code>cg.identifier.doi</code> field, so I added those</li>
+<li>Then I imported those 2398 items in two batches (to deal with memory issues):</li>
+</ul></li>
+</ul>
+
+<pre><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx1024m&quot;
+$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive.csv
+$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive2.csv
+</code></pre>
+
+<ul>
+<li>I noticed there are many items that use HTTP instead of HTTPS for their Google Books URL, and some missing HTTP entirely:</li>
+</ul>
+
+<pre><code>dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
+ count
+-------
+   785
+dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
+ count
+-------
+     4
+</code></pre>
+
+<ul>
+<li>I think I should fix that as well as some other garbage values like &ldquo;test&rdquo; and &ldquo;dspace.ilri.org&rdquo; etc:</li>
+</ul>
+
+<pre><code>dspace=# begin;
+dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
+UPDATE 785
+dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
+UPDATE 4
+dspace=# update metadatavalue set text_value='https://books.google.com/books?id=meF1CLdPSF4C' where resource_type_id=2 and metadata_field_id=222 and text_value='meF1CLdPSF4C';
+UPDATE 1
+dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=222 and metadata_value_id in (2299312, 10684, 10700, 996403);
+DELETE 4
+dspace=# commit;
+</code></pre>
+
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docs/404.html

@@ -26,7 +26,7 @@
 <meta name="twitter:card" content="summary"/>
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 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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docs/categories/index.html

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 <meta name="twitter:card" content="summary"/>
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docs/categories/notes/index.html

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 <meta name="twitter:card" content="summary"/>
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 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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 <meta name="twitter:card" content="summary"/>
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 <meta name="twitter:card" content="summary"/>
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docs/cgiar-library-migration/index.html

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 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="CGIAR Library Migration"/>
 <meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
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docs/index.html

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 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="CGSpace Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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docs/page/2/index.html

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 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="CGSpace Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.42.1" />
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docs/page/3/index.html

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 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="CGSpace Notes"/>
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docs/page/4/index.html

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 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="CGSpace Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.42.1" />
+<meta name="generator" content="Hugo 0.42.2" />
 
 
     

docs/posts/index.html

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 <meta name="twitter:card" content="summary"/>
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docs/posts/page/2/index.html

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 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Posts"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.42.1" />
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docs/posts/page/3/index.html

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 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Posts"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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docs/posts/page/4/index.html

@@ -26,7 +26,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Posts"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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docs/sitemap.xml

@@ -4,7 +4,7 @@
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/2018-07/</loc>
-    <lastmod>2018-07-01T18:05:01+03:00</lastmod>
+    <lastmod>2018-07-02T17:33:38+03:00</lastmod>
   </url>
   
   <url>
@@ -174,7 +174,7 @@
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/</loc>
-    <lastmod>2018-07-01T18:05:01+03:00</lastmod>
+    <lastmod>2018-07-02T17:33:38+03:00</lastmod>
     <priority>0</priority>
   </url>
   
@@ -185,7 +185,7 @@
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
-    <lastmod>2018-07-01T18:05:01+03:00</lastmod>
+    <lastmod>2018-07-02T17:33:38+03:00</lastmod>
     <priority>0</priority>
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@@ -197,13 +197,13 @@
   
   <url>
     <loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
-    <lastmod>2018-07-01T18:05:01+03:00</lastmod>
+    <lastmod>2018-07-02T17:33:38+03:00</lastmod>
     <priority>0</priority>
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   <url>
     <loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
-    <lastmod>2018-07-01T18:05:01+03:00</lastmod>
+    <lastmod>2018-07-02T17:33:38+03:00</lastmod>
     <priority>0</priority>
   </url>
   

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docs/tags/notes/index.html

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docs/tags/notes/page/2/index.html

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docs/tags/notes/page/3/index.html

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docs/tags/notes/page/4/index.html

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