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Add notes for 2018-07-03

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Alan Orth 2018-07-03 14:37:30 +03:00
parent 172cda49e8
commit f72d67f67a
Signed by: alanorth
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58 changed files with 154 additions and 64 deletions
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42
content/posts/2018-07.md
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@ -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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@ -53,7 +53,7 @@ $ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspac
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docs/2015-12/index.html
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@ -55,7 +55,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
"/>
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@ -45,7 +45,7 @@ Update GitHub wiki for documentation of maintenance tasks.
"/>
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@ -59,7 +59,7 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
"/>
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docs/2016-03/index.html
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@ -45,7 +45,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
"/>
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@ -49,7 +49,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
"/>
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@ -53,7 +53,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
"/>
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@ -51,7 +51,7 @@ Working on second phase of metadata migration, looks like this will work for mov
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docs/2016-07/index.html
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@ -67,7 +67,7 @@ In this case the select query was showing 95 results before the update
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docs/2016-08/index.html
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@ -61,7 +61,7 @@ $ git rebase -i dspace-5.5
"/>
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docs/2016-09/index.html
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@ -53,7 +53,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
"/>
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docs/2016-10/index.html
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@ -61,7 +61,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
"/>
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docs/2016-11/index.html
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@ -45,7 +45,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
"/>
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docs/2016-12/index.html
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@ -69,7 +69,7 @@ Another worrying error from dspace.log is:
"/>
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2
docs/2017-01/index.html
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@ -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
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@ -73,7 +73,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
"/>
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2
docs/2017-03/index.html
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@ -77,7 +77,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
"/>
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2
docs/2017-04/index.html
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@ -63,7 +63,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
"/>
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<meta name="generator" content="Hugo 0.42.2" />

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@ -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."/>
<meta name="generator" content="Hugo 0.42.1" />
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@ -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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@ -57,7 +57,7 @@ We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the
"/>
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@ -77,7 +77,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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docs/2017-09/index.html
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@ -53,7 +53,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account
"/>
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docs/2017-10/index.html
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@ -57,7 +57,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
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docs/2017-11/index.html
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@ -77,7 +77,7 @@ COPY 54701
"/>
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docs/2017-12/index.html
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@ -47,7 +47,7 @@ The list of connections to XMLUI and REST API for today:
"/>
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docs/2018-01/index.html
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@ -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
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@ -47,7 +47,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
"/>
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docs/2018-03/index.html
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@ -41,7 +41,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
"/>
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docs/2018-04/index.html
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@ -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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@ -55,7 +55,7 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
"/>
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@ -83,7 +83,7 @@ sys 2m7.289s
"/>
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docs/2018-07/index.html
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@ -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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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="404 Page not found"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.42.2" />

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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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@ -26,7 +26,7 @@
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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"/>
<meta name="twitter:title" content="Categories"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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@ -29,7 +29,7 @@
<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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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
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@ -26,7 +26,7 @@
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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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@ -26,7 +26,7 @@
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@ -26,7 +26,7 @@
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<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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@ -26,7 +26,7 @@
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@ -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>
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@ -174,7 +174,7 @@
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<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 @@
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