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Add notes for 2018-07-15
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@ -334,4 +334,50 @@ dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue
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COPY 4518
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```
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## 2018-07-15
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- Run all system updates on CGSpace, add latest metadata changes from last week, and start the Linode instance upgrade
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- After the upgrade I see we have more disk space available in the instance's dashboard, so I shut the instance down and resized it from 392GB to 650GB
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- The resize was very quick (less than one minute) and after booting the instance back up I now have 631GB for the root filesystem (with 267GB available)!
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- Peter had asked a question about how mapped items are displayed in the Altmetric dashboard
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- For example, [10568/82810](10568/82810) is mapped to four collections, but only shows up in one "department" in their dashboard
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- Altmetric help said that [according to OAI that item is only in one department](https://cgspace.cgiar.org/oai/request?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:cgspace.cgiar.org:10568/82810)
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- I noticed that indeed there was only one collection listed, so I forced an OAI re-import on CGSpace:
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```
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$ dspace oai import -c
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OAI 2.0 manager action started
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Clearing index
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Index cleared
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Using full import.
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Full import
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100 items imported so far...
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200 items imported so far...
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...
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73900 items imported so far...
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Total: 73925 items
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Purging cached OAI responses.
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OAI 2.0 manager action ended. It took 697 seconds.
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```
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- Now I see four colletions in OAI for that item!
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- I need to ask the dspace-tech mailing list if the nightly OAI import catches the case of old items that have had metadata or mappings change
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- ICARDA sent me a list of the ORCID iDs they have in the MEL system and it looks like almost 150 are new and unique to us!
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```
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$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq | wc -l
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1020
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$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq | wc -l
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1158
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```
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- I combined the two lists and regenerated the names for all our the ORCID iDs using my [resolve-orcids.py](https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b) script:
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```
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$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2018-07-15-orcid-ids.txt
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$ ./resolve-orcids.py -i /tmp/2018-07-15-orcid-ids.txt -o /tmp/2018-07-15-resolved-orcids.txt -d
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```
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- Help Udana from WLE understand some Altmetrics concepts
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<!-- vim: set sw=2 ts=2: -->
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@ -30,7 +30,7 @@ There is insufficient memory for the Java Runtime Environment to continue.
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<meta property="article:published_time" content="2018-07-01T12:56:54+03:00"/>
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<meta property="article:modified_time" content="2018-07-12T17:07:17+03:00"/>
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<meta property="article:modified_time" content="2018-07-13T19:45:58+03:00"/>
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@ -71,9 +71,9 @@ There is insufficient memory for the Java Runtime Environment to continue.
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"@type": "BlogPosting",
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"headline": "July, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-07/",
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"wordCount": "2226",
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"wordCount": "2561",
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"datePublished": "2018-07-01T12:56:54+03:00",
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"dateModified": "2018-07-12T17:07:17+03:00",
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"dateModified": "2018-07-13T19:45:58+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -516,6 +516,57 @@ $ csvcut -c 1 < /tmp/affiliations.csv > /tmp/affiliations-1.csv
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COPY 4518
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</code></pre>
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<h2 id="2018-07-15">2018-07-15</h2>
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<ul>
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<li>Run all system updates on CGSpace, add latest metadata changes from last week, and start the Linode instance upgrade</li>
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<li>After the upgrade I see we have more disk space available in the instance’s dashboard, so I shut the instance down and resized it from 392GB to 650GB</li>
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<li>The resize was very quick (less than one minute) and after booting the instance back up I now have 631GB for the root filesystem (with 267GB available)!</li>
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<li>Peter had asked a question about how mapped items are displayed in the Altmetric dashboard</li>
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<li>For example, <a href="10568/82810"><sup>10568</sup>⁄<sub>82810</sub></a> is mapped to four collections, but only shows up in one “department” in their dashboard</li>
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<li>Altmetric help said that <a href="https://cgspace.cgiar.org/oai/request?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:cgspace.cgiar.org:10568/82810">according to OAI that item is only in one department</a></li>
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<li>I noticed that indeed there was only one collection listed, so I forced an OAI re-import on CGSpace:</li>
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</ul>
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<pre><code>$ dspace oai import -c
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OAI 2.0 manager action started
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Clearing index
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Index cleared
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Using full import.
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Full import
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100 items imported so far...
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200 items imported so far...
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...
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73900 items imported so far...
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Total: 73925 items
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Purging cached OAI responses.
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OAI 2.0 manager action ended. It took 697 seconds.
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</code></pre>
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<ul>
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<li>Now I see four colletions in OAI for that item!</li>
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<li>I need to ask the dspace-tech mailing list if the nightly OAI import catches the case of old items that have had metadata or mappings change</li>
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<li>ICARDA sent me a list of the ORCID iDs they have in the MEL system and it looks like almost 150 are new and unique to us!</li>
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</ul>
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<pre><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq | wc -l
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1020
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$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq | wc -l
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1158
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</code></pre>
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<ul>
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<li>I combined the two lists and regenerated the names for all our the ORCID iDs using my <a href="https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b">resolve-orcids.py</a> script:</li>
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</ul>
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<pre><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2018-07-15-orcid-ids.txt
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$ ./resolve-orcids.py -i /tmp/2018-07-15-orcid-ids.txt -o /tmp/2018-07-15-resolved-orcids.txt -d
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</code></pre>
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<ul>
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<li>Help Udana from WLE understand some Altmetrics concepts</li>
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</ul>
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<!-- vim: set sw=2 ts=2: -->
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@ -37,7 +37,7 @@ Disallow: /cgspace-notes/2015-12/
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Disallow: /cgspace-notes/2015-11/
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Disallow: /cgspace-notes/
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Disallow: /cgspace-notes/categories/
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Disallow: /cgspace-notes/tags/notes/
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Disallow: /cgspace-notes/categories/notes/
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Disallow: /cgspace-notes/tags/notes/
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Disallow: /cgspace-notes/posts/
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Disallow: /cgspace-notes/tags/
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@ -4,7 +4,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2018-07/</loc>
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<lastmod>2018-07-12T17:07:17+03:00</lastmod>
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<lastmod>2018-07-13T19:45:58+03:00</lastmod>
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</url>
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<url>
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@ -174,7 +174,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2018-07-12T17:07:17+03:00</lastmod>
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<lastmod>2018-07-13T19:45:58+03:00</lastmod>
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<priority>0</priority>
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</url>
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@ -183,27 +183,27 @@
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2018-07-12T17:07:17+03:00</lastmod>
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
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<lastmod>2018-03-09T22:10:33+02:00</lastmod>
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2018-07-13T19:45:58+03:00</lastmod>
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
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<lastmod>2018-07-12T17:07:17+03:00</lastmod>
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<lastmod>2018-07-13T19:45:58+03:00</lastmod>
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
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<lastmod>2018-07-12T17:07:17+03:00</lastmod>
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<lastmod>2018-07-13T19:45:58+03:00</lastmod>
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<priority>0</priority>
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</url>
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