Update notes for 2017-05-08

content/post/2017-05.md

@@ -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

public/2017-05/index.html

@@ -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>

public/sitemap.xml

@@ -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>