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Alan Orth 2017-05-10 23:44:44 +03:00
parent fe6726122a
commit 4d443e60e1
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
3 changed files with 62 additions and 12 deletions
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28
content/post/2017-05.md
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@ -64,8 +64,8 @@ $ ./fix-metadata-values.py -i ccafs-flagships-may7.csv -f cg.subject.ccafs -t co
```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit"
$ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e aorth@mjanja.ch -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done
```
- Note that in submission mode DSpace ignores the handle specified in `mets.xml` in the zip file, so you need to turn that off with `-o ignoreHandle=false`
@ -98,7 +98,31 @@ Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violate
Detail: Key (handle_id)=(80928) already exists.
```
- I think those errors actually come from me running the `update-sequences.sql` script while Tomcat/DSpace are running
- Apparently you need to stop Tomcat!
## 2017-05-10
- Atmire says they are willing to extend the ORCID implementation, and I've asked them to provide a quote
- I clarified that the scope of the implementation should be that ORCIDs are stored in the database and exposed via REST / API like other fields
- Finally finished importing all the CGIAR Library content, final method was:
```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit"
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2517/10947-2517.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2515/10947-2515.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2516/10947-2516.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ [dspace]/bin/dspace packager -s -t AIP -o ignoreHandle=false -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done
```
- Basically, import the smaller communities using recursive AIP import (with `skipIfParentMissing`)
- Then, for the larger collection, create the community, collections, and items separately, ingesting the items one by one
- The `-XX:-UseGCOverheadLimit` JVM option helps with some issues in large imports
- After this I ran the `update-sequences.sql` script (with Tomcat shut down), and cleaned up the 200+ blank metadata records:
```
dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
```

36
public/2017-05/index.html
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@ -13,7 +13,7 @@
<meta property="article:published_time" content="2017-05-01T16:21:52&#43;02:00"/>
<meta property="article:modified_time" content="2017-05-10T00:16:49&#43;03:00"/>
<meta property="article:modified_time" content="2017-05-10T11:20:27&#43;03:00"/>
@ -45,9 +45,9 @@
"@type": "BlogPosting",
"headline": "May, 2017",
"url": "https://alanorth.github.io/cgspace-notes/2017-05/",
"wordCount": "827",
"wordCount": "1037",
"datePublished": "2017-05-01T16:21:52&#43;02:00",
"dateModified": "2017-05-10T00:16:49&#43;03:00",
"dateModified": "2017-05-10T11:20:27&#43;03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -189,8 +189,8 @@
<pre><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit&quot;
$ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e aorth@mjanja.ch -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done
</code></pre>
<ul>
@ -230,13 +230,39 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
Detail: Key (handle_id)=(80928) already exists.
</code></pre>
<ul>
<li>I think those errors actually come from me running the <code>update-sequences.sql</code> script while Tomcat/DSpace are running</li>
<li>Apparently you need to stop Tomcat!</li>
</ul>
<h2 id="2017-05-10">2017-05-10</h2>
<ul>
<li>Atmire says they are willing to extend the ORCID implementation, and I&rsquo;ve asked them to provide a quote</li>
<li>I clarified that the scope of the implementation should be that ORCIDs are stored in the database and exposed via REST / API like other fields</li>
<li>Finally finished importing all the CGIAR Library content, final method was:</li>
</ul>
<pre><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit&quot;
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2517/10947-2517.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2515/10947-2515.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2516/10947-2516.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ [dspace]/bin/dspace packager -s -t AIP -o ignoreHandle=false -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done
</code></pre>
<ul>
<li>Basically, import the smaller communities using recursive AIP import (with <code>skipIfParentMissing</code>)</li>
<li>Then, for the larger collection, create the community, collections, and items separately, ingesting the items one by one</li>
<li>The <code>-XX:-UseGCOverheadLimit</code> JVM option helps with some issues in large imports</li>
<li>After this I ran the <code>update-sequences.sql</code> script (with Tomcat shut down), and cleaned up the 200+ blank metadata records:</li>
</ul>
<pre><code>dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
</code></pre>

10
public/sitemap.xml
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@ -4,7 +4,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2017-05/</loc>
<lastmod>2017-05-10T00:16:49+03:00</lastmod>
<lastmod>2017-05-10T11:20:27+03:00</lastmod>
</url>
<url>
@ -99,7 +99,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2017-05-10T00:16:49+03:00</lastmod>
<lastmod>2017-05-10T11:20:27+03:00</lastmod>
<priority>0</priority>
</url>
@ -110,19 +110,19 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2017-05-10T00:16:49+03:00</lastmod>
<lastmod>2017-05-10T11:20:27+03:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/post/</loc>
<lastmod>2017-05-10T00:16:49+03:00</lastmod>
<lastmod>2017-05-10T11:20:27+03:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2017-05-10T00:16:49+03:00</lastmod>
<lastmod>2017-05-10T11:20:27+03:00</lastmod>
<priority>0</priority>
</url>