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Add notes for 2018-04-04

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Alan Orth 2018-04-04 15:57:34 +03:00
parent 05a15ba3cd
commit 56626d1245
Signed by: alanorth
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59 changed files with 129 additions and 71 deletions
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2
content/posts/2018-03.md
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@ -127,7 +127,7 @@ if(isBlank(value), "Hernan Ceballos: 0000-0002-8744-7918", value + "||Hernan Ceb
- One thing that bothers me is that this won't honor author order
- It might be better to do batches of these in PostgreSQL with a script that takes the `place` column of an author into account when setting the `cg.creator.id`
- I wrote a Python script to read the author names and ORCID identifiers from CSV and create matching `cg.creator.id` fieldsa: [add-orcid-identifiers-csv.py ](https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050)
- I wrote a Python script to read the author names and ORCID identifiers from CSV and create matching `cg.creator.id` fields: [add-orcid-identifiers-csv.py ](https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050)
- The CSV should have two columns: author name and ORCID identifier:
```

31
content/posts/2018-04.md
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@ -25,3 +25,34 @@ Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" jav
- For some reason Listings and Reports is not giving any results for any queries now...
- I posted a message on Yammer to ask if people are using the Duplicate Check step from the Metadata Quality Module
- Help Lili Szilagyi with a question about statistics on some CCAFS items
## 2018-04-04
- Peter noticed that there were still some old CRP names on CGSpace, because I hadn't forced the Discovery index to be updated after I fixed the others last week
- For completeness I re-ran the CRP corrections on CGSpace:
```
$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
```
- Then started a full Discovery index:
```
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx1024m'
$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
```
- Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme's items
- I used my [add-orcid-identifiers-csv.py](https://gist.githubusercontent.com/alanorth/a49d85cd9c5dea89cddbe809813a7050/raw/f67b6e45a9a940732882ae4bb26897a9b245ef31/add-orcid-identifiers-csv.py) script:
```
$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
```
- The CSV format of `jtohme-2018-04-04.csv` was:
```csv
dc.contributor.author,cg.creator.id
"Tohme, Joseph M.",Joe Tohme: 0000-0003-2765-7101
```

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@ -53,7 +53,7 @@ $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspac
"/>
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@ -55,7 +55,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
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@ -45,7 +45,7 @@ Update GitHub wiki for documentation of maintenance tasks.
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@ -59,7 +59,7 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
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@ -45,7 +45,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
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@ -49,7 +49,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
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@ -53,7 +53,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
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@ -51,7 +51,7 @@ Working on second phase of metadata migration, looks like this will work for mov
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@ -67,7 +67,7 @@ In this case the select query was showing 95 results before the update
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docs/2016-08/index.html
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@ -61,7 +61,7 @@ $ git rebase -i dspace-5.5
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@ -53,7 +53,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
"/>
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@ -61,7 +61,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
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@ -45,7 +45,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
"/>
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docs/2016-12/index.html
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@ -69,7 +69,7 @@ Another worrying error from dspace.log is:
"/>
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@ -45,7 +45,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
"/>
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@ -73,7 +73,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
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@ -77,7 +77,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
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@ -63,7 +63,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
"/>
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@ -29,7 +29,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2017"/>
<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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@ -29,7 +29,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2017"/>
<meta name="twitter:description" content="2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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@ -57,7 +57,7 @@ We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the
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@ -77,7 +77,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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@ -53,7 +53,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account
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@ -57,7 +57,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
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@ -77,7 +77,7 @@ COPY 54701
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@ -47,7 +47,7 @@ The list of connections to XMLUI and REST API for today:
"/>
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docs/2018-01/index.html
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@ -185,7 +185,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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docs/2018-02/index.html
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@ -47,7 +47,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
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15
docs/2018-03/index.html
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@ -20,7 +20,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
<meta property="article:published_time" content="2018-03-02T16:07:54&#43;02:00"/>
<meta property="article:modified_time" content="2018-03-28T22:01:13&#43;03:00"/>
<meta property="article:modified_time" content="2018-04-04T15:14:21&#43;03:00"/>
@ -41,7 +41,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
"/>
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@ -51,9 +51,9 @@ Export a CSV of the IITA community metadata for Martin Mueller
"@type": "BlogPosting",
"headline": "March, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-03/",
"wordCount": "2961",
"wordCount": "2960",
"datePublished": "2018-03-02T16:07:54&#43;02:00",
"dateModified": "2018-03-28T22:01:13&#43;03:00",
"dateModified": "2018-04-04T15:14:21&#43;03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -255,7 +255,7 @@ UPDATE 2309
<ul>
<li>One thing that bothers me is that this won&rsquo;t honor author order</li>
<li>It might be better to do batches of these in PostgreSQL with a script that takes the <code>place</code> column of an author into account when setting the <code>cg.creator.id</code></li>
<li>I wrote a Python script to read the author names and ORCID identifiers from CSV and create matching <code>cg.creator.id</code> fieldsa: <a href="https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050">add-orcid-identifiers-csv.py </a></li>
<li>I wrote a Python script to read the author names and ORCID identifiers from CSV and create matching <code>cg.creator.id</code> fields: <a href="https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050">add-orcid-identifiers-csv.py </a></li>
<li>The CSV should have two columns: author name and ORCID identifier:</li>
</ul>
@ -536,11 +536,6 @@ COPY 56156
<ul>
<li>Afterwards we&rsquo;ll want to do some batch tagging of ORCID identifiers to these names</li>
</ul>
<h2 id="2018-03-20-1">2018-03-20</h2>
<ul>
<li>CGSpace crashed again this afternoon, I&rsquo;m not sure of the cause but there are a lot of SQL errors in the DSpace log:</li>
</ul>

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@ -43,7 +43,7 @@ Catalina logs at least show some memory errors yesterday:
"/>
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@ -53,7 +53,7 @@ Catalina logs at least show some memory errors yesterday:
"@type": "BlogPosting",
"headline": "April, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-04/",
"wordCount": "118",
"wordCount": "253",
"datePublished": "2018-04-01T16:13:54&#43;02:00",
"dateModified": "2018-04-01T17:21:41&#43;03:00",
"author": {
@ -145,6 +145,41 @@ Exception in thread &quot;ContainerBackgroundProcessor[StandardEngine[Catalina]]
<li>Help Lili Szilagyi with a question about statistics on some CCAFS items</li>
</ul>
<h2 id="2018-04-04">2018-04-04</h2>
<ul>
<li>Peter noticed that there were still some old CRP names on CGSpace, because I hadn&rsquo;t forced the Discovery index to be updated after I fixed the others last week</li>
<li>For completeness I re-ran the CRP corrections on CGSpace:</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
</code></pre>
<ul>
<li>Then started a full Discovery index:</li>
</ul>
<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx1024m'
$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
</code></pre>
<ul>
<li>Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme&rsquo;s items</li>
<li>I used my <a href="https://gist.githubusercontent.com/alanorth/a49d85cd9c5dea89cddbe809813a7050/raw/f67b6e45a9a940732882ae4bb26897a9b245ef31/add-orcid-identifiers-csv.py">add-orcid-identifiers-csv.py</a> script:</li>
</ul>
<pre><code>$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
</code></pre>
<ul>
<li>The CSV format of <code>jtohme-2018-04-04.csv</code> was:</li>
</ul>
<pre><code class="language-csv">dc.contributor.author,cg.creator.id
&quot;Tohme, Joseph M.&quot;,Joe Tohme: 0000-0003-2765-7101
</code></pre>

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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="404 Page not found"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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@ -41,9 +41,6 @@
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-CoMzlF7G4xk3ftqRr7leobnWP85AuISUJljMFjtTG/UHyP/&#43;bBwWAvBlXkB4VQQk" crossorigin="anonymous">
<!-- RSS 2.0 feed -->
<link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />

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