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Update notes for 2017-05-08

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Alan Orth 2017-05-09 00:43:02 +03:00
parent 18346b3b90
commit 3a1e203aa6
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GPG Key ID: 0FB860CC9C45B1B9
3 changed files with 35 additions and 8 deletions
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13
content/post/2017-05.md
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@ -56,6 +56,19 @@ $ ./fix-metadata-values.py -i ccafs-flagships-may7.csv -f cg.subject.ccafs -t co
- Start working on CGIAR Library migration
- We decided to use AIP export to preserve the hierarchies and handles of communities and collections
- When ingesting some collections I was getting `java.lang.OutOfMemoryError: GC overhead limit exceeded`, which can be solved by disabling the GC timeout with `-XX:-UseGCOverheadLimit`
- Other times I was getting an error about heap space, so I kept bumping the RAM allocation by 512MB each time (up to 4096m!) it crashed
- This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using `dspace cleanup -v`, or else you'll run out of disk space
- In the end I realized it's better to use submission mode (`-s`) to ingest the community object as a single AIP without its children, followed by each of the collections:
```
$ 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
```
- 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`
- Give feedback to CIFOR about their data quality:
- Suggestion: uppercase dc.subject, cg.coverage.region, and cg.coverage.subregion in your crosswalk so they match CGSpace and therefore can be faceted / reported on easier
- Suggestion: use CGSpace's CRP names (cg.contributor.crp), see: dspace/config/input-forms.xml

20
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="2017-05-08T17:51:55&#43;03:00"/>
<meta property="article:modified_time" content="2017-05-08T20:20:52&#43;03:00"/>
@ -45,9 +45,9 @@
"@type": "BlogPosting",
"headline": "May, 2017",
"url": "https://alanorth.github.io/cgspace-notes/2017-05/",
"wordCount": "464",
"wordCount": "653",
"datePublished": "2017-05-01T16:21:52&#43;02:00",
"dateModified": "2017-05-08T17:51:55&#43;03:00",
"dateModified": "2017-05-08T20:20:52&#43;03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -181,6 +181,20 @@
<ul>
<li>Start working on CGIAR Library migration</li>
<li>We decided to use AIP export to preserve the hierarchies and handles of communities and collections</li>
<li>When ingesting some collections I was getting <code>java.lang.OutOfMemoryError: GC overhead limit exceeded</code>, which can be solved by disabling the GC timeout with <code>-XX:-UseGCOverheadLimit</code></li>
<li>Other times I was getting an error about heap space, so I kept bumping the RAM allocation by 512MB each time (up to 4096m!) it crashed</li>
<li>This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using <code>dspace cleanup -v</code>, or else you&rsquo;ll run out of disk space</li>
<li>In the end I realized it&rsquo;s better to use submission mode (<code>-s</code>) to ingest the community object as a single AIP without its children, followed by each of the collections:</li>
</ul>
<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
</code></pre>
<ul>
<li>Note that in submission mode DSpace ignores the handle specified in <code>mets.xml</code> in the zip file, so you need to turn that off with <code>-o ignoreHandle=false</code></li>
<li>Give feedback to CIFOR about their data quality:
<ul>

10
public/sitemap.xml
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@ -4,7 +4,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2017-05/</loc>
<lastmod>2017-05-08T17:51:55+03:00</lastmod>
<lastmod>2017-05-08T20:20:52+03:00</lastmod>
</url>
<url>
@ -99,7 +99,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2017-05-08T17:51:55+03:00</lastmod>
<lastmod>2017-05-08T20:20:52+03:00</lastmod>
<priority>0</priority>
</url>
@ -110,19 +110,19 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2017-05-08T17:51:55+03:00</lastmod>
<lastmod>2017-05-08T20:20:52+03:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/post/</loc>
<lastmod>2017-05-08T17:51:55+03:00</lastmod>
<lastmod>2017-05-08T20:20:52+03:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2017-05-08T17:51:55+03:00</lastmod>
<lastmod>2017-05-08T20:20:52+03:00</lastmod>
<priority>0</priority>
</url>