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Add notes for 2019-05-05
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404.htmlcategories
cgiar-library-migration
index.htmlindex.xmlpage
posts
sitemap.xmltags
@ -15,7 +15,7 @@
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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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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.55.3" />
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<meta name="generator" content="Hugo 0.55.5" />
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@ -101,18 +101,16 @@
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<h2 id="2018-07-01">2018-07-01</h2>
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<ul>
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<li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li>
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</ul>
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<li><p>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</p>
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<pre><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
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</code></pre>
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</code></pre></li>
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<ul>
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<li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li>
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</ul>
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<li><p>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</p>
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<pre><code>There is insufficient memory for the Java Runtime Environment to continue.
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</code></pre>
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</code></pre></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-07/'>Read more →</a>
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</article>
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@ -139,23 +137,23 @@
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<li>There seems to be a problem with the CUA and L&R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn’t build</li>
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</ul></li>
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<li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li>
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<li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li>
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</ul>
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<li><p>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</p>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
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</code></pre>
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</code></pre></li>
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<ul>
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<li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></li>
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<li>Time to index ~70,000 items on CGSpace:</li>
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</ul>
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<li><p>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></p></li>
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<li><p>Time to index ~70,000 items on CGSpace:</p>
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<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
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real 74m42.646s
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user 8m5.056s
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sys 2m7.289s
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</code></pre>
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</code></pre></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-06/'>Read more →</a>
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</article>
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@ -279,26 +277,25 @@ sys 2m7.289s
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<li>I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary</li>
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<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
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<li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li>
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<li>And just before that I see this:</li>
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</ul>
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<li><p>And just before that I see this:</p>
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<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Ah hah! So the pool was actually empty!</li>
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<li>I need to increase that, let’s try to bump it up from 50 to 75</li>
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<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</li>
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<li>I notice this error quite a few times in dspace.log:</li>
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</ul>
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<li><p>Ah hah! So the pool was actually empty!</p></li>
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<li><p>I need to increase that, let’s try to bump it up from 50 to 75</p></li>
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<li><p>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</p></li>
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<li><p>I notice this error quite a few times in dspace.log:</p>
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<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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</code></pre>
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</code></pre></li>
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<ul>
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<li>And there are many of these errors every day for the past month:</li>
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</ul>
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<li><p>And there are many of these errors every day for the past month:</p>
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<pre><code>$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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@ -344,10 +341,9 @@ dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains</li>
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<li><p>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains</p></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
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</article>
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@ -400,20 +396,18 @@ dspace.log.2018-01-02:34
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<h2 id="2017-11-02">2017-11-02</h2>
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<ul>
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<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
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</ul>
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<li><p>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</p>
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<pre><code># grep -c "CORE" /var/log/nginx/access.log
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0
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
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</ul>
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<li><p>Generate list of authors on CGSpace for Peter to go through and correct:</p>
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<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
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COPY 54701
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</code></pre>
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</code></pre></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
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</article>
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@ -434,15 +428,14 @@ COPY 54701
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<h2 id="2017-10-01">2017-10-01</h2>
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<ul>
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<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
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</ul>
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<li><p>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</p>
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<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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</code></pre>
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</code></pre></li>
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<ul>
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<li>There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li>
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<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
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<li><p>There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</p></li>
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<li><p>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</p></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
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</article>
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@ -15,7 +15,7 @@
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||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="CGSpace Notes"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.55.3" />
|
||||
<meta name="generator" content="Hugo 0.55.5" />
|
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|
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@ -261,11 +261,12 @@
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<ul>
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<li>Remove redundant/duplicate text in the DSpace submission license</li>
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<li>Testing the CMYK patch on a collection with 650 items:</li>
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</ul>
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<li><p>Testing the CMYK patch on a collection with 650 items:</p>
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<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt
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</code></pre>
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</code></pre></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
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</article>
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@ -300,12 +301,13 @@
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<li>Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI</li>
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<li>Filed an issue on DSpace issue tracker for the <code>filter-media</code> bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: <a href="https://jira.duraspace.org/browse/DS-3516">DS-3516</a></li>
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<li>Discovered that the ImageMagic <code>filter-media</code> plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK</li>
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<li>Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see <a href="https://cgspace.cgiar.org/handle/10568/51999"><sup>10568</sup>⁄<sub>51999</sub></a>):</li>
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</ul>
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<li><p>Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see <a href="https://cgspace.cgiar.org/handle/10568/51999"><sup>10568</sup>⁄<sub>51999</sub></a>):</p>
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<pre><code>$ identify ~/Desktop/alc_contrastes_desafios.jpg
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/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
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</code></pre>
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</code></pre></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-03/'>Read more →</a>
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</article>
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@ -326,23 +328,22 @@
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<h2 id="2017-02-07">2017-02-07</h2>
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<ul>
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<li>An item was mapped twice erroneously again, so I had to remove one of the mappings manually:</li>
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</ul>
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<li><p>An item was mapped twice erroneously again, so I had to remove one of the mappings manually:</p>
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<pre><code>dspace=# select * from collection2item where item_id = '80278';
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id | collection_id | item_id
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id | collection_id | item_id
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-------+---------------+---------
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92551 | 313 | 80278
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92550 | 313 | 80278
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90774 | 1051 | 80278
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92551 | 313 | 80278
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92550 | 313 | 80278
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90774 | 1051 | 80278
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(3 rows)
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dspace=# delete from collection2item where id = 92551 and item_id = 80278;
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DELETE 1
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</code></pre>
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</code></pre></li>
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<ul>
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<li>Create issue on GitHub to track the addition of CCAFS Phase II project tags (<a href="https://github.com/ilri/DSpace/issues/301">#301</a>)</li>
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<li>Looks like we’ll be using <code>cg.identifier.ccafsprojectpii</code> as the field name</li>
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<li><p>Create issue on GitHub to track the addition of CCAFS Phase II project tags (<a href="https://github.com/ilri/DSpace/issues/301">#301</a>)</p></li>
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<li><p>Looks like we’ll be using <code>cg.identifier.ccafsprojectpii</code> as the field name</p></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-02/'>Read more →</a>
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</article>
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@ -15,7 +15,7 @@
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<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="CGSpace Notes"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.55.3" />
|
||||
<meta name="generator" content="Hugo 0.55.5" />
|
||||
|
||||
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@ -102,20 +102,21 @@
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<ul>
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<li>CGSpace was down for five hours in the morning while I was sleeping</li>
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<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
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</ul>
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<li><p>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</p>
|
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<pre><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
|
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail="dc.title", transactionID="TX157907838689377964651674089851855413607")
|
||||
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail="THUMBNAIL", transactionID="TX157907838689377964651674089851855413607")
|
||||
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail="-1", transactionID="TX157907838689377964651674089851855413607")
|
||||
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
|
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</code></pre>
|
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</code></pre></li>
|
||||
|
||||
<ul>
|
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<li>I see thousands of them in the logs for the last few months, so it’s not related to the DSpace 5.5 upgrade</li>
|
||||
<li>I’ve raised a ticket with Atmire to ask</li>
|
||||
<li>Another worrying error from dspace.log is:</li>
|
||||
<li><p>I see thousands of them in the logs for the last few months, so it’s not related to the DSpace 5.5 upgrade</p></li>
|
||||
|
||||
<li><p>I’ve raised a ticket with Atmire to ask</p></li>
|
||||
|
||||
<li><p>Another worrying error from dspace.log is:</p></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2016-12/'>Read more →</a>
|
||||
</article>
|
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@ -168,11 +169,12 @@
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<li>ORCIDs only</li>
|
||||
<li>ORCIDs plus normal authors</li>
|
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</ul></li>
|
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<li>I exported a random item’s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
|
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</ul>
|
||||
|
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<li><p>I exported a random item’s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</p>
|
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|
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<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
|
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</code></pre>
|
||||
</code></pre></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
|
||||
</article>
|
||||
|
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@ -196,11 +198,12 @@
|
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<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
|
||||
<li>Discuss how the migration of CGIAR’s Active Directory to a flat structure will break our LDAP groups in DSpace</li>
|
||||
<li>We had been using <code>DC=ILRI</code> to determine whether a user was ILRI or not</li>
|
||||
<li>It looks like we might be able to use OUs now, instead of DCs:</li>
|
||||
</ul>
|
||||
|
||||
<li><p>It looks like we might be able to use OUs now, instead of DCs:</p>
|
||||
|
||||
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
|
||||
</code></pre>
|
||||
</code></pre></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2016-09/'>Read more →</a>
|
||||
</article>
|
||||
|
||||
@ -226,13 +229,14 @@
|
||||
<li>Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more</li>
|
||||
<li>bower stuff is a dead end, waste of time, too many issues</li>
|
||||
<li>Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of <code>fonts</code>)</li>
|
||||
<li>Start working on DSpace 5.1 → 5.5 port:</li>
|
||||
</ul>
|
||||
|
||||
<li><p>Start working on DSpace 5.1 → 5.5 port:</p>
|
||||
|
||||
<pre><code>$ git checkout -b 55new 5_x-prod
|
||||
$ git reset --hard ilri/5_x-prod
|
||||
$ git rebase -i dspace-5.5
|
||||
</code></pre>
|
||||
</code></pre></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2016-08/'>Read more →</a>
|
||||
</article>
|
||||
|
||||
@ -254,19 +258,18 @@ $ git rebase -i dspace-5.5
|
||||
|
||||
<ul>
|
||||
<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
|
||||
<li>I think this query should find and replace all authors that have “,” at the end of their names:</li>
|
||||
</ul>
|
||||
|
||||
<li><p>I think this query should find and replace all authors that have “,” at the end of their names:</p>
|
||||
|
||||
<pre><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
|
||||
UPDATE 95
|
||||
dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
|
||||
text_value
|
||||
text_value
|
||||
------------
|
||||
(0 rows)
|
||||
</code></pre>
|
||||
</code></pre></li>
|
||||
|
||||
<ul>
|
||||
<li>In this case the select query was showing 95 results before the update</li>
|
||||
<li><p>In this case the select query was showing 95 results before the update</p></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2016-07/'>Read more →</a>
|
||||
</article>
|
||||
@ -317,12 +320,13 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
|
||||
<ul>
|
||||
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
|
||||
<li>I have blocked access to the API now</li>
|
||||
<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
|
||||
</ul>
|
||||
|
||||
<li><p>There are 3,000 IPs accessing the REST API in a 24-hour period!</p>
|
||||
|
||||
<pre><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
|
||||
3168
|
||||
</code></pre>
|
||||
</code></pre></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2016-05/'>Read more →</a>
|
||||
</article>
|
||||
|
||||
|
||||
@ -15,7 +15,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="CGSpace Notes"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.55.3" />
|
||||
<meta name="generator" content="Hugo 0.55.5" />
|
||||
|
||||
|
||||
|
||||
@ -156,15 +156,15 @@
|
||||
<h2 id="2015-12-02">2015-12-02</h2>
|
||||
|
||||
<ul>
|
||||
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
|
||||
</ul>
|
||||
<li><p>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</p>
|
||||
|
||||
<pre><code># cd /home/dspacetest.cgiar.org/log
|
||||
# ls -lh dspace.log.2015-11-18*
|
||||
-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
|
||||
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
|
||||
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
|
||||
</code></pre>
|
||||
</code></pre></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2015-12/'>Read more →</a>
|
||||
</article>
|
||||
|
||||
@ -187,12 +187,13 @@
|
||||
<ul>
|
||||
<li>CGSpace went down</li>
|
||||
<li>Looks like DSpace exhausted its PostgreSQL connection pool</li>
|
||||
<li>Last week I had increased the limit from 30 to 60, which seemed to help, but now there are many more idle connections:</li>
|
||||
</ul>
|
||||
|
||||
<li><p>Last week I had increased the limit from 30 to 60, which seemed to help, but now there are many more idle connections:</p>
|
||||
|
||||
<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
|
||||
78
|
||||
</code></pre>
|
||||
</code></pre></li>
|
||||
</ul>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2015-11/'>Read more →</a>
|
||||
</article>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user