Add notes for 2018-06-27

2024-11-22 14:45:03 +01:00 · 2018-06-27 17:16:24 +03:00 · 2018-06-27 17:16:24 +03:00 · a6f5f0c6b2
commit a6f5f0c6b2
parent 6ecb0c84d6
4 changed files with 97 additions and 14 deletions
--- a/content/posts/2018-06.md
+++ b/content/posts/2018-06.md
@ -308,4 +308,43 @@ dc.contributor.author,cg.creator.id
 - It's actually only a warning and it also appears in the logs on DSpace Test (which is currently running DSpace 5.5), so I need to keep troubleshooting
 - Ah, I think I just need to run `dspace oai import`

+## 2018-06-27
+
+- Vika from CIFOR sent back his annotations on the duplicates for the "CIFOR_May_9" archive import that I sent him last week
+- I'll have to figure out how to separate those we're keeping, deleting, and mapping into CIFOR's archive collection
+- First, get the 62 deletes from Vika's file and remove them from the collection:
+
+```
+$ grep delete 2018-06-22-cifor-duplicates.txt | grep -o -E '[0-9]{5}\/[0-9]{5}' > cifor-handle-to-delete.txt
+$ wc -l cifor-handle-to-delete.txt
+62 cifor-handle-to-delete.txt
+$ wc -l 10568-92904.csv
+2461 10568-92904.csv
+$ while read line; do sed -i "\#$line#d" 10568-92904.csv; done < cifor-handle-to-delete.txt
+$ wc -l 10568-92904.csv
+2399 10568-92904.csv
+```
+
+- This iterates over the handles for deletion and uses `sed` with an alternative pattern delimiter of '#' (which must be escaped), because the pattern itself contains a '/'
+- The mapped ones will be difficult because we need their internal IDs in order to map them, and there are 50 of them:
+
+```
+$ grep map 2018-06-22-cifor-duplicates.txt | grep -o -E '[0-9]{5}\/[0-9]{5}' > cifor-handle-to-map.txt
+$ wc -l cifor-handle-to-map.txt
+50 cifor-handle-to-map.txt
+```
+
+- I can either get them from the databse, or programatically export the metadata using `dspace metadata-export -i 10568/xxxxx`...
+- Oooh, I can export the items one by one, concatenate them together, remove the headers, and extract the `id` and `collection` columns using [csvkit](https://csvkit.readthedocs.io/):
+
+```
+$ while read line; do filename=${line/\//-}.csv; dspace metadata-export -i $line -f $filename; done < /tmp/cifor-handle-to-map.txt
+$ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 > map-to-cifor-archive.csv
+```
+
+- Then I can use Open Refine to add the "CIFOR Archive" collection to the mappings
+- Importing the 2398 items via `dspace metadata-import` ends up with a Java garbage collection error, so I think I need to do it in batches of 1,000
+- After deleting the 62 duplicates, mapping the 50 items from elsewhere in CGSpace, and uploading 2,398 unique items, there are a total of 2,448 items added in this batch
+- I'll let Abenet take one last look and then move them to CGSpace
+
 <!-- vim: set sw=2 ts=2: -->
--- a/docs/2018-06/index.html
+++ b/docs/2018-06/index.html
@ -41,7 +41,7 @@ sys     2m7.289s

 <meta property="article:published_time" content="2018-06-04T19:49:54-07:00"/>

-<meta property="article:modified_time" content="2018-06-24T17:38:07&#43;03:00"/>
+<meta property="article:modified_time" content="2018-06-26T17:17:55&#43;03:00"/>



@ -93,9 +93,9 @@ sys     2m7.289s
  "@type": "BlogPosting",
  "headline": "June, 2018",
  "url": "https://alanorth.github.io/cgspace-notes/2018-06/",
-  "wordCount": "2420",
+  "wordCount": "2734",
  "datePublished": "2018-06-04T19:49:54-07:00",
-  "dateModified": "2018-06-24T17:38:07&#43;03:00",
+  "dateModified": "2018-06-26T17:17:55&#43;03:00",
  "author": {
    "@type": "Person",
    "name": "Alan Orth"
@ -517,6 +517,50 @@ Done.
 <li>Ah, I think I just need to run <code>dspace oai import</code></li>
 </ul>

+<h2 id="2018-06-27">2018-06-27</h2>
+
+<ul>
+<li>Vika from CIFOR sent back his annotations on the duplicates for the &ldquo;CIFOR_May_9&rdquo; archive import that I sent him last week</li>
+<li>I&rsquo;ll have to figure out how to separate those we&rsquo;re keeping, deleting, and mapping into CIFOR&rsquo;s archive collection</li>
+<li>First, get the 62 deletes from Vika&rsquo;s file and remove them from the collection:</li>
+</ul>
+
+<pre><code>$ grep delete 2018-06-22-cifor-duplicates.txt | grep -o -E '[0-9]{5}\/[0-9]{5}' &gt; cifor-handle-to-delete.txt
+$ wc -l cifor-handle-to-delete.txt
+62 cifor-handle-to-delete.txt
+$ wc -l 10568-92904.csv
+2461 10568-92904.csv
+$ while read line; do sed -i &quot;\#$line#d&quot; 10568-92904.csv; done &lt; cifor-handle-to-delete.txt
+$ wc -l 10568-92904.csv
+2399 10568-92904.csv
+</code></pre>
+
+<ul>
+<li>This iterates over the handles for deletion and uses <code>sed</code> with an alternative pattern delimiter of &lsquo;#&rsquo; (which must be escaped), because the pattern itself contains a &lsquo;/&rsquo;</li>
+<li>The mapped ones will be difficult because we need their internal IDs in order to map them, and there are 50 of them:</li>
+</ul>
+
+<pre><code>$ grep map 2018-06-22-cifor-duplicates.txt | grep -o -E '[0-9]{5}\/[0-9]{5}' &gt; cifor-handle-to-map.txt
+$ wc -l cifor-handle-to-map.txt
+50 cifor-handle-to-map.txt
+</code></pre>
+
+<ul>
+<li>I can either get them from the databse, or programatically export the metadata using <code>dspace metadata-export -i 10568/xxxxx</code>&hellip;</li>
+<li>Oooh, I can export the items one by one, concatenate them together, remove the headers, and extract the <code>id</code> and <code>collection</code> columns using <a href="https://csvkit.readthedocs.io/">csvkit</a>:</li>
+</ul>
+
+<pre><code>$ while read line; do filename=${line/\//-}.csv; dspace metadata-export -i $line -f $filename; done &lt; /tmp/cifor-handle-to-map.txt
+$ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 &gt; map-to-cifor-archive.csv
+</code></pre>
+
+<ul>
+<li>Then I can use Open Refine to add the &ldquo;CIFOR Archive&rdquo; collection to the mappings</li>
+<li>Importing the 2398 items via <code>dspace metadata-import</code> ends up with a Java garbage collection error, so I think I need to do it in batches of 1,000</li>
+<li>After deleting the 62 duplicates, mapping the 50 items from elsewhere in CGSpace, and uploading 2,398 unique items, there are a total of 2,448 items added in this batch</li>
+<li>I&rsquo;ll let Abenet take one last look and then move them to CGSpace</li>
+</ul>
+
 <!-- vim: set sw=2 ts=2: -->

  
--- a/docs/robots.txt
+++ b/docs/robots.txt
@ -36,7 +36,7 @@ Disallow: /cgspace-notes/2015-12/
 Disallow: /cgspace-notes/2015-11/
 Disallow: /cgspace-notes/
 Disallow: /cgspace-notes/categories/
-Disallow: /cgspace-notes/tags/notes/
 Disallow: /cgspace-notes/categories/notes/
+Disallow: /cgspace-notes/tags/notes/
 Disallow: /cgspace-notes/posts/
 Disallow: /cgspace-notes/tags/
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@ -4,7 +4,7 @@
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/2018-06/</loc>
-    <lastmod>2018-06-24T17:38:07+03:00</lastmod>
+    <lastmod>2018-06-26T17:17:55+03:00</lastmod>
  </url>
  
  <url>
@ -169,7 +169,7 @@
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/</loc>
-    <lastmod>2018-06-24T17:38:07+03:00</lastmod>
+    <lastmod>2018-06-26T17:17:55+03:00</lastmod>
    <priority>0</priority>
  </url>
  
@ -178,27 +178,27 @@
    <priority>0</priority>
  </url>
  
-  <url>
-    <loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
-    <lastmod>2018-06-24T17:38:07+03:00</lastmod>
-    <priority>0</priority>
-  </url>
-  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
    <lastmod>2018-03-09T22:10:33+02:00</lastmod>
    <priority>0</priority>
  </url>
  
+  <url>
+    <loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
+    <lastmod>2018-06-26T17:17:55+03:00</lastmod>
+    <priority>0</priority>
+  </url>
+  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
-    <lastmod>2018-06-24T17:38:07+03:00</lastmod>
+    <lastmod>2018-06-26T17:17:55+03:00</lastmod>
    <priority>0</priority>
  </url>
  
  <url>
    <loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
-    <lastmod>2018-06-24T17:38:07+03:00</lastmod>
+    <lastmod>2018-06-26T17:17:55+03:00</lastmod>
    <priority>0</priority>
  </url>