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Add notes for 2020-08-19
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@ -432,12 +432,6 @@ $ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
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$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2016
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```
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- Then I see there are 849,000 docs with `id: -1` and `type: 5` so I should purge those too probably:
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```
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$ curl -s "http://localhost:8081/solr/statistics-2017/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:\-1</query></delete>'
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```
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- Altmetric asked for a dump of CGSpace's OAI "sets" so they can update their affiliation mappings
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- I did it in a kinda ghetto way:
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@ -450,4 +444,55 @@ $ for num in {0..1300..100}; do cat /tmp/$num.xml >> /tmp/cgspace-oai-sets.xml;
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- This produces one file that has all the sets, albeit with 14 pages of responses concatenated into one document, but that's how theirs was in the first place...
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- Help Bizu with a restricted item for CIAT
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## 2020-08-16
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- The com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI script that was processing 2015 records last night started spitting shit tons of errors and created 120GB of logs...
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- I looked at a few of the UIDs that it was having problems with and they were unmigrated ones... so I purged them in 2015 and all the rest of the statistics cores
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```
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$ curl -s "http://localhost:8081/solr/statistics-2015/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:/.*unmigrated.*/</query></delete>'
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...
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$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:/.*unmigrated.*/</query></delete>'
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```
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## 2020-08-19
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- I tested the DSpace 5 and DSpace 6 versions of the [country code tagger curation task](https://github.com/ilri/cgspace-java-helpers) and noticed a few things
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- The DSpace 5.8 version finishes in 2 hours and 1 minute
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||||
- The DSpace 6.3 version ran for over 12 hours and didn't even finish (I killed it)
|
||||
- Furthermore, it seems that each item is curated once for each collection it appears in, causing about 115,000 items to be processed, even though we only have about 87,000
|
||||
- I had been running the tasks on the entire repository with `-i 10568/0`, but I think I might need to try again with the special `all` option before writing to the dspace-tech mailing list for help
|
||||
- Actually I just tested the `all` option on DSpace 5.8 and it still does many of the items multiple times, once for each of their mappings
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- I finished the Atmire stats processing on all cores on DSpace Test:
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- statistics:
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||||
- 2,040,385 docs: 2h 28m 49s
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||||
- statistics-2019:
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- 8,960,000 docs: 12h 7s
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||||
- 1,780,575 docs: 2h 7m 29s
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- statistics-2018:
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- 2,200,000 docs: 12h 1m 11s
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- 2,100,000 docs: 12h 4m 19s
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- ?
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- statistics-2017:
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- 1,970,000 docs: 12h 5m 45s
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- 2,000,000 docs: 12h 5m 38s
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- 1,312,674 docs: 4h 14m 23s
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- statistics-2016:
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- 1,669,020 docs: 12h 4m 3s
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- 1,650,000 docs: 12h 7m 40s
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- 850,611 docs: 44m 52s
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- statistics-2014:
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- 4,832,334 docs: 3h 53m 41s
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||||
- statistics-2013:
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||||
- 4,509,891 docs: 3h 18m 44s
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||||
- statistics-2012:
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||||
- 3,716,857 docs: 2h 36m 21s
|
||||
- statistics-2011:
|
||||
- 1,645,426 docs: 1h 11m 41s
|
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- As far as I can tell, the processing became much faster once I purged all the unmigrated records
|
||||
- It took about six days for the processing according to the times above, though 2015 is missing... hmm
|
||||
- Now I am testing the Atmire Listings and Reports
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- On both my local test and DSpace Test I get no results when searching for "Orth, A." and "Orth, Alan" or even Delia Grace, but the Discovery index is up to date and I have eighteen items...
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- I sent a message to Atmire...
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<!-- vim: set sw=2 ts=2: -->
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@ -19,7 +19,7 @@ It is class based so I can easily add support for other vocabularies, and the te
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-08/" />
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<meta property="article:published_time" content="2020-08-02T15:35:54+03:00" />
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<meta property="article:modified_time" content="2020-08-13T17:56:39+03:00" />
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<meta property="article:modified_time" content="2020-08-14T11:22:16+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="August, 2020"/>
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@ -43,9 +43,9 @@ It is class based so I can easily add support for other vocabularies, and the te
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"@type": "BlogPosting",
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"headline": "August, 2020",
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"url": "https://alanorth.github.io/cgspace-notes/2020-08/",
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"wordCount": "2800",
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"wordCount": "3168",
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"datePublished": "2020-08-02T15:35:54+03:00",
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"dateModified": "2020-08-13T17:56:39+03:00",
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"dateModified": "2020-08-14T11:22:16+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -599,10 +599,6 @@ Caused by: java.lang.NullPointerException
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$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
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$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2016
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</code></pre><ul>
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<li>Then I see there are 849,000 docs with <code>id: -1</code> and <code>type: 5</code> so I should purge those too probably:</li>
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</ul>
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<pre><code>$ curl -s "http://localhost:8081/solr/statistics-2017/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:\-1</query></delete>'
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</code></pre><ul>
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<li>Altmetric asked for a dump of CGSpace’s OAI “sets” so they can update their affiliation mappings
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<ul>
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<li>I did it in a kinda ghetto way:</li>
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@ -616,6 +612,96 @@ $ for num in {0..1300..100}; do cat /tmp/$num.xml >> /tmp/cgspace-oai-sets
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<li>This produces one file that has all the sets, albeit with 14 pages of responses concatenated into one document, but that’s how theirs was in the first place…</li>
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<li>Help Bizu with a restricted item for CIAT</li>
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</ul>
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<h2 id="2020-08-16">2020-08-16</h2>
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<ul>
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<li>The com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI script that was processing 2015 records last night started spitting shit tons of errors and created 120GB of logs…</li>
|
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<li>I looked at a few of the UIDs that it was having problems with and they were unmigrated ones… so I purged them in 2015 and all the rest of the statistics cores</li>
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</ul>
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<pre><code>$ curl -s "http://localhost:8081/solr/statistics-2015/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:/.*unmigrated.*/</query></delete>'
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...
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$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:/.*unmigrated.*/</query></delete>'
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</code></pre><h2 id="2020-08-19">2020-08-19</h2>
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<ul>
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<li>I tested the DSpace 5 and DSpace 6 versions of the <a href="https://github.com/ilri/cgspace-java-helpers">country code tagger curation task</a> and noticed a few things
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<ul>
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<li>The DSpace 5.8 version finishes in 2 hours and 1 minute</li>
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<li>The DSpace 6.3 version ran for over 12 hours and didn’t even finish (I killed it)</li>
|
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<li>Furthermore, it seems that each item is curated once for each collection it appears in, causing about 115,000 items to be processed, even though we only have about 87,000</li>
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</ul>
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</li>
|
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<li>I had been running the tasks on the entire repository with <code>-i 10568/0</code>, but I think I might need to try again with the special <code>all</code> option before writing to the dspace-tech mailing list for help
|
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<ul>
|
||||
<li>Actually I just tested the <code>all</code> option on DSpace 5.8 and it still does many of the items multiple times, once for each of their mappings</li>
|
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</ul>
|
||||
</li>
|
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<li>I finished the Atmire stats processing on all cores on DSpace Test:
|
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<ul>
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<li>statistics:
|
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<ul>
|
||||
<li>2,040,385 docs: 2h 28m 49s</li>
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</ul>
|
||||
</li>
|
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<li>statistics-2019:
|
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<ul>
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<li>8,960,000 docs: 12h 7s</li>
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<li>1,780,575 docs: 2h 7m 29s</li>
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</ul>
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</li>
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<li>statistics-2018:
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<ul>
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<li>2,200,000 docs: 12h 1m 11s</li>
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<li>2,100,000 docs: 12h 4m 19s</li>
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<li>?</li>
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</ul>
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</li>
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<li>statistics-2017:
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<ul>
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<li>1,970,000 docs: 12h 5m 45s</li>
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<li>2,000,000 docs: 12h 5m 38s</li>
|
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<li>1,312,674 docs: 4h 14m 23s</li>
|
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</ul>
|
||||
</li>
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<li>statistics-2016:
|
||||
<ul>
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<li>1,669,020 docs: 12h 4m 3s</li>
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||||
<li>1,650,000 docs: 12h 7m 40s</li>
|
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<li>850,611 docs: 44m 52s</li>
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</ul>
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</li>
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<li>statistics-2014:
|
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<ul>
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<li>4,832,334 docs: 3h 53m 41s</li>
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</ul>
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</li>
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<li>statistics-2013:
|
||||
<ul>
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<li>4,509,891 docs: 3h 18m 44s</li>
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</ul>
|
||||
</li>
|
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<li>statistics-2012:
|
||||
<ul>
|
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<li>3,716,857 docs: 2h 36m 21s</li>
|
||||
</ul>
|
||||
</li>
|
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<li>statistics-2011:
|
||||
<ul>
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<li>1,645,426 docs: 1h 11m 41s</li>
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</ul>
|
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</li>
|
||||
</ul>
|
||||
</li>
|
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<li>As far as I can tell, the processing became much faster once I purged all the unmigrated records
|
||||
<ul>
|
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<li>It took about six days for the processing according to the times above, though 2015 is missing… hmm</li>
|
||||
</ul>
|
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</li>
|
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<li>Now I am testing the Atmire Listings and Reports
|
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<ul>
|
||||
<li>On both my local test and DSpace Test I get no results when searching for “Orth, A.” and “Orth, Alan” or even Delia Grace, but the Discovery index is up to date and I have eighteen items…</li>
|
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<li>I sent a message to Atmire…</li>
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</ul>
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</li>
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</ul>
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||||
<!-- raw HTML omitted -->
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@ -9,7 +9,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
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<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
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||||
<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
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||||
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||||
<meta name="twitter:card" content="summary"/>
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||||
<meta name="twitter:title" content="Categories"/>
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||||
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||||
@ -9,7 +9,7 @@
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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||||
<meta property="og:type" content="website" />
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||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
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<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
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||||
<meta name="twitter:card" content="summary"/>
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||||
<meta name="twitter:title" content="Notes"/>
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||||
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||||
@ -9,7 +9,7 @@
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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||||
<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
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<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
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||||
<meta name="twitter:card" content="summary"/>
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||||
<meta name="twitter:title" content="Notes"/>
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||||
@ -9,7 +9,7 @@
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="Notes"/>
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||||
@ -9,7 +9,7 @@
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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||||
<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
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|
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<meta name="twitter:card" content="summary"/>
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||||
<meta name="twitter:title" content="Notes"/>
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||||
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||||
@ -9,7 +9,7 @@
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
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<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
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||||
<meta name="twitter:card" content="summary"/>
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||||
<meta name="twitter:title" content="CGSpace Notes"/>
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||||
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||||
@ -9,7 +9,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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||||
<meta name="twitter:card" content="summary"/>
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||||
<meta name="twitter:title" content="CGSpace Notes"/>
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||||
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||||
@ -9,7 +9,7 @@
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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|
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="CGSpace Notes"/>
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||||
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@ -9,7 +9,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="CGSpace Notes"/>
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@ -9,7 +9,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="CGSpace Notes"/>
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@ -9,7 +9,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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|
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="CGSpace Notes"/>
|
||||
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@ -9,7 +9,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
|
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|
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|
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|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
||||
|
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@ -9,7 +9,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
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<meta property="og:type" content="website" />
|
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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||||
<meta name="twitter:card" content="summary"/>
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||||
<meta name="twitter:title" content="Posts"/>
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@ -9,7 +9,7 @@
|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
|
||||
<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
|
||||
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
|
||||
<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
|
||||
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
|
||||
<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
|
||||
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
|
||||
<meta property="og:updated_time" content="2020-08-13T17:56:39+03:00" />
|
||||
<meta property="og:updated_time" content="2020-08-14T11:22:16+03:00" />
|
||||
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
||||
|
||||
@ -4,27 +4,27 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2020-08/</loc>
|
||||
<lastmod>2020-08-13T17:56:39+03:00</lastmod>
|
||||
<lastmod>2020-08-14T11:22:16+03:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
|
||||
<lastmod>2020-08-13T17:56:39+03:00</lastmod>
|
||||
<lastmod>2020-08-14T11:22:16+03:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2020-08-13T17:56:39+03:00</lastmod>
|
||||
<lastmod>2020-08-14T11:22:16+03:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2020-08-13T17:56:39+03:00</lastmod>
|
||||
<lastmod>2020-08-14T11:22:16+03:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2020-08-13T17:56:39+03:00</lastmod>
|
||||
<lastmod>2020-08-14T11:22:16+03:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user