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Add notes for 2019-11-28
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@ -8,9 +8,8 @@
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<meta property="og:title" content="March, 2016" />
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<meta property="og:description" content="2016-03-02
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Looking at issues with author authorities on CGSpace
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For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module
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For some reason we still have the index-lucene-update cron job active on CGSpace, but I'm pretty sure we don't need it as of the latest few versions of Atmire's Listings and Reports module
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Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server
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" />
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<meta property="og:type" content="article" />
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@ -22,12 +21,11 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
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<meta name="twitter:title" content="March, 2016"/>
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<meta name="twitter:description" content="2016-03-02
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Looking at issues with author authorities on CGSpace
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For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module
|
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For some reason we still have the index-lucene-update cron job active on CGSpace, but I'm pretty sure we don't need it as of the latest few versions of Atmire's Listings and Reports module
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Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server
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"/>
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<meta name="generator" content="Hugo 0.59.1" />
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<meta name="generator" content="Hugo 0.60.0" />
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@ -108,112 +106,86 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
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</p>
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</header>
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<h2 id="2016-03-02">2016-03-02</h2>
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<h2 id="20160302">2016-03-02</h2>
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<ul>
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<li>Looking at issues with author authorities on CGSpace</li>
|
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<li>For some reason we still have the <code>index-lucene-update</code> cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module</li>
|
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<li>For some reason we still have the <code>index-lucene-update</code> cron job active on CGSpace, but I'm pretty sure we don't need it as of the latest few versions of Atmire's Listings and Reports module</li>
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<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
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</ul>
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<h2 id="2016-03-07">2016-03-07</h2>
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<h2 id="20160307">2016-03-07</h2>
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<ul>
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<li>Troubleshooting the issues with the slew of commits for Atmire modules in <a href="https://github.com/ilri/DSpace/pull/182">#182</a></li>
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<li>Their changes on <code>5_x-dev</code> branch work, but it is messy as hell with merge commits and old branch base</li>
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<li>When I rebase their branch on the latest <code>5_x-prod</code> I get blank white pages</li>
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<li>I identified one commit that causes the issue and let them know</li>
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<li><p>Restart DSpace Test, as it seems to have crashed after Sisay tried to import some CSV or zip or something:</p>
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<pre><code>Exception in thread "Lucene Merge Thread #19" org.apache.lucene.index.MergePolicy$MergeException: java.io.IOException: No space left on device
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</code></pre></li>
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<li>Restart DSpace Test, as it seems to have crashed after Sisay tried to import some CSV or zip or something:</li>
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</ul>
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<h2 id="2016-03-08">2016-03-08</h2>
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<pre><code>Exception in thread "Lucene Merge Thread #19" org.apache.lucene.index.MergePolicy$MergeException: java.io.IOException: No space left on device
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</code></pre><h2 id="20160308">2016-03-08</h2>
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<ul>
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<li>Add a few new filters to Atmire’s Listings and Reports module (<a href="https://github.com/ilri/DSpace/issues/180">#180</a>)</li>
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<li>Add a few new filters to Atmire's Listings and Reports module (<a href="https://github.com/ilri/DSpace/issues/180">#180</a>)</li>
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<li>We had also wanted to add a few to the Content and Usage module but I have to ask the editors which ones they were</li>
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</ul>
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<h2 id="2016-03-10">2016-03-10</h2>
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<h2 id="20160310">2016-03-10</h2>
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<ul>
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<li>Disable the lucene cron job on CGSpace as it shouldn’t be needed anymore</li>
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<li>Disable the lucene cron job on CGSpace as it shouldn't be needed anymore</li>
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<li>Discuss ORCiD and duplicate authors on Yammer</li>
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<li>Request new documentation for Atmire CUA and L&R modules, as ours are from 2013</li>
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<li>Walk Sisay through some data cleaning workflows in OpenRefine</li>
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<li>Start cleaning up the configuration for Atmire’s CUA module (<a href="https://github.com/ilri/DSpace/issues/185">#184</a>)</li>
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<li>Start cleaning up the configuration for Atmire's CUA module (<a href="https://github.com/ilri/DSpace/issues/185">#184</a>)</li>
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<li>It is very messed up because some labels are incorrect, fields are missing, etc</li>
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</ul>
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<p><img src="/cgspace-notes/2016/03/cua-label-mixup.png" alt="Mixed up label in Atmire CUA" /></p>
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<p><img src="/cgspace-notes/2016/03/cua-label-mixup.png" alt="Mixed up label in Atmire CUA"></p>
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<ul>
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<li>Update documentation for Atmire modules</li>
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</ul>
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<h2 id="2016-03-11">2016-03-11</h2>
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<h2 id="20160311">2016-03-11</h2>
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<ul>
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<li>As I was looking at the CUA config I realized our Discovery config is all messed up and confusing</li>
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<li>I’ve opened an issue to track some of that work (<a href="https://github.com/ilri/DSpace/issues/186">#186</a>)</li>
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<li>I've opened an issue to track some of that work (<a href="https://github.com/ilri/DSpace/issues/186">#186</a>)</li>
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<li>I did some major cleanup work on Discovery and XMLUI stuff related to the <code>dc.type</code> indexes (<a href="https://github.com/ilri/DSpace/pull/187">#187</a>)</li>
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<li>We had been confusing <code>dc.type</code> (a Dublin Core value) with <code>dc.type.output</code> (a value we invented) for a few years and it had permeated all aspects of our data, indexes, item displays, etc.</li>
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<li>There is still some more work to be done to remove references to old <code>outputtype</code> and <code>output</code></li>
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</ul>
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<h2 id="2016-03-14">2016-03-14</h2>
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<h2 id="20160314">2016-03-14</h2>
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<ul>
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<li>Fix some items that had invalid dates (I noticed them in the log during a re-indexing)</li>
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<li>Reset <code>search.index.*</code> to the default, as it is only used by Lucene (deprecated by Discovery in DSpace 5.x): <a href="https://github.com/ilri/DSpace/pull/188">#188</a></li>
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<li>Make titles in Discovery and Browse by more consistent (singular, sentence case, etc) (<a href="https://github.com/ilri/DSpace/issues/186">#186</a>)</li>
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<li>Also four or so center-specific subject strings were missing for Discovery</li>
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</ul>
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<p><img src="/cgspace-notes/2016/03/missing-xmlui-string.png" alt="Missing XMLUI string" /></p>
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<h2 id="2016-03-15">2016-03-15</h2>
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<p><img src="/cgspace-notes/2016/03/missing-xmlui-string.png" alt="Missing XMLUI string"></p>
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<h2 id="20160315">2016-03-15</h2>
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<ul>
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<li>Create simple theme for new AVCD community just for a unique Google Tracking ID (<a href="https://github.com/ilri/DSpace/pull/191">#191</a>)</li>
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</ul>
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<h2 id="2016-03-16">2016-03-16</h2>
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<h2 id="20160316">2016-03-16</h2>
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<ul>
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<li>Still having problems deploying Atmire’s CUA updates and fixes from January!</li>
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<li>Still having problems deploying Atmire's CUA updates and fixes from January!</li>
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<li>More discussion on the GitHub issue here: <a href="https://github.com/ilri/DSpace/pull/182">https://github.com/ilri/DSpace/pull/182</a></li>
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<li>Clean up Atmire CUA config (<a href="https://github.com/ilri/DSpace/pull/193">#193</a>)</li>
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<li>Help Sisay with some PostgreSQL queries to clean up the incorrect <code>dc.contributor.corporateauthor</code> field</li>
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<li><p>I noticed that we have some weird values in <code>dc.language</code>:</p>
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<pre><code># select * from metadatavalue where metadata_field_id=37;
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metadata_value_id | resource_id | metadata_field_id | text_value | text_lang | place | authority | confidence | resource_type_id
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-------------------+-------------+-------------------+------------+-----------+-------+-----------+------------+------------------
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1942571 | 35342 | 37 | hi | | 1 | | -1 | 2
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1942468 | 35345 | 37 | hi | | 1 | | -1 | 2
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1942479 | 35337 | 37 | hi | | 1 | | -1 | 2
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1942505 | 35336 | 37 | hi | | 1 | | -1 | 2
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1942519 | 35338 | 37 | hi | | 1 | | -1 | 2
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1942535 | 35340 | 37 | hi | | 1 | | -1 | 2
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1942555 | 35341 | 37 | hi | | 1 | | -1 | 2
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1942588 | 35343 | 37 | hi | | 1 | | -1 | 2
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1942610 | 35346 | 37 | hi | | 1 | | -1 | 2
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1942624 | 35347 | 37 | hi | | 1 | | -1 | 2
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1942639 | 35339 | 37 | hi | | 1 | | -1 | 2
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</code></pre></li>
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<li><p>It seems this <code>dc.language</code> field isn’t really used, but we should delete these values</p></li>
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<li><p>Also, <code>dc.language.iso</code> has some weird values, like “En” and “English”</p></li>
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<li>I noticed that we have some weird values in <code>dc.language</code>:</li>
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</ul>
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<h2 id="2016-03-17">2016-03-17</h2>
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<pre><code># select * from metadatavalue where metadata_field_id=37;
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metadata_value_id | resource_id | metadata_field_id | text_value | text_lang | place | authority | confidence | resource_type_id
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-------------------+-------------+-------------------+------------+-----------+-------+-----------+------------+------------------
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||||
1942571 | 35342 | 37 | hi | | 1 | | -1 | 2
|
||||
1942468 | 35345 | 37 | hi | | 1 | | -1 | 2
|
||||
1942479 | 35337 | 37 | hi | | 1 | | -1 | 2
|
||||
1942505 | 35336 | 37 | hi | | 1 | | -1 | 2
|
||||
1942519 | 35338 | 37 | hi | | 1 | | -1 | 2
|
||||
1942535 | 35340 | 37 | hi | | 1 | | -1 | 2
|
||||
1942555 | 35341 | 37 | hi | | 1 | | -1 | 2
|
||||
1942588 | 35343 | 37 | hi | | 1 | | -1 | 2
|
||||
1942610 | 35346 | 37 | hi | | 1 | | -1 | 2
|
||||
1942624 | 35347 | 37 | hi | | 1 | | -1 | 2
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1942639 | 35339 | 37 | hi | | 1 | | -1 | 2
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</code></pre><ul>
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<li>It seems this <code>dc.language</code> field isn't really used, but we should delete these values</li>
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<li>Also, <code>dc.language.iso</code> has some weird values, like “En” and “English”</li>
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</ul>
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<h2 id="20160317">2016-03-17</h2>
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<ul>
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<li>It turns out <code>hi</code> is the ISO 639 language code for Hindi, but these should be in <code>dc.language.iso</code> instead of <code>dc.language</code></li>
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<li>I fixed the eleven items with <code>hi</code> as well as some using the incorrect <code>vn</code> for Vietnamese</li>
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@ -221,108 +193,83 @@ metadata_value_id | resource_id | metadata_field_id | text_value | text_lang | p
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<li>Re-sync CGSpace database to DSpace Test for Atmire to do some tests about the problematic CUA patches</li>
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<li>The patches work fine with a clean database, so the error was caused by some mismatch in CUA versions and the database during my testing</li>
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</ul>
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<h2 id="2016-03-18">2016-03-18</h2>
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<h2 id="20160318">2016-03-18</h2>
|
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<ul>
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<li>Merge Atmire fixes into <code>5_x-prod</code></li>
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<li>Discuss thumbnails with Francesca from Bioversity</li>
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<li>Some of their items end up with thumbnails that have a big white border around them:</li>
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</ul>
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<p><img src="/cgspace-notes/2016/03/bioversity-thumbnail-bad.jpg" alt="Excessive whitespace in thumbnail" /></p>
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<p><img src="/cgspace-notes/2016/03/bioversity-thumbnail-bad.jpg" alt="Excessive whitespace in thumbnail"></p>
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<ul>
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<li>Turns out we can add <code>-trim</code> to the GraphicsMagick options to trim the whitespace</li>
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</ul>
|
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<p><img src="/cgspace-notes/2016/03/bioversity-thumbnail-good.jpg" alt="Trimmed thumbnail" /></p>
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|
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<p><img src="/cgspace-notes/2016/03/bioversity-thumbnail-good.jpg" alt="Trimmed thumbnail"></p>
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<ul>
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<li><p>Command used:</p>
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<pre><code>$ gm convert -trim -quality 82 -thumbnail x300 -flatten Descriptor\ for\ Butia_EN-2015_2021.pdf\[0\] cover.jpg
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</code></pre></li>
|
||||
|
||||
<li><p>Also, it looks like adding <code>-sharpen 0x1.0</code> really improves the quality of the image for only a few KB</p></li>
|
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<li>Command used:</li>
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</ul>
|
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|
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<h2 id="2016-03-21">2016-03-21</h2>
|
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|
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<pre><code>$ gm convert -trim -quality 82 -thumbnail x300 -flatten Descriptor\ for\ Butia_EN-2015_2021.pdf\[0\] cover.jpg
|
||||
</code></pre><ul>
|
||||
<li>Also, it looks like adding <code>-sharpen 0x1.0</code> really improves the quality of the image for only a few KB</li>
|
||||
</ul>
|
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<h2 id="20160321">2016-03-21</h2>
|
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<ul>
|
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<li>Fix 66 site errors in Google’s webmaster tools</li>
|
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<li>Fix 66 site errors in Google's webmaster tools</li>
|
||||
<li>I looked at a bunch of them and they were old URLs, weird things linked from non-existent items, etc, so I just marked them all as fixed</li>
|
||||
<li>We also have 1,300 “soft 404” errors for URLs like: <a href="https://cgspace.cgiar.org/handle/10568/440/browse?type=bioversity">https://cgspace.cgiar.org/handle/10568/440/browse?type=bioversity</a></li>
|
||||
<li>I’ve marked them as fixed as well since the ones I tested were working fine</li>
|
||||
<li>I've marked them as fixed as well since the ones I tested were working fine</li>
|
||||
<li>This raises another question, as many of these pages are linked from Discovery search results and might create a duplicate content problem…</li>
|
||||
<li>Results pages like this give items that Google already knows from the sitemap: <a href="https://cgspace.cgiar.org/discover?filtertype=author&filter_relational_operator=equals&filter=Orth%2C+A">https://cgspace.cgiar.org/discover?filtertype=author&filter_relational_operator=equals&filter=Orth%2C+A</a>.</li>
|
||||
<li>There are some access denied errors on JSPUI links (of course! we forbid them!), but I’m not sure why Google is trying to index them…</li>
|
||||
<li>There are some access denied errors on JSPUI links (of course! we forbid them!), but I'm not sure why Google is trying to index them…</li>
|
||||
<li>For example:
|
||||
|
||||
<ul>
|
||||
<li>This: <a href="https://cgspace.cgiar.org/jspui/bitstream/10568/809/1/main-page.pdf">https://cgspace.cgiar.org/jspui/bitstream/10568/809/1/main-page.pdf</a></li>
|
||||
<li>Linked from: <a href="https://cgspace.cgiar.org/jspui/handle/10568/809">https://cgspace.cgiar.org/jspui/handle/10568/809</a></li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>I will mark these errors as resolved because they are returning HTTP 403 on purpose, for a long time!</li>
|
||||
<li>Google says the first time it saw this particular error was September 29, 2015… so maybe it accidentally saw it somehow…</li>
|
||||
<li>On a related note, we have 51,000 items indexed from the sitemap, but 500,000 items in the Google index, so we DEFINITELY have a problem with duplicate content</li>
|
||||
</ul>
|
||||
|
||||
<p><img src="/cgspace-notes/2016/03/google-index.png" alt="CGSpace pages in Google index" /></p>
|
||||
|
||||
<p><img src="/cgspace-notes/2016/03/google-index.png" alt="CGSpace pages in Google index"></p>
|
||||
<ul>
|
||||
<li>Turns out this is a problem with DSpace’s <code>robots.txt</code>, and there’s a Jira ticket since December, 2015: <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li>
|
||||
<li>Turns out this is a problem with DSpace's <code>robots.txt</code>, and there's a Jira ticket since December, 2015: <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li>
|
||||
<li>I am not sure if I want to apply it yet</li>
|
||||
<li>For now I’ve just set a bunch of these dynamic pages to not appear in search results by using the URL Parameters tool in Webmaster Tools</li>
|
||||
<li>For now I've just set a bunch of these dynamic pages to not appear in search results by using the URL Parameters tool in Webmaster Tools</li>
|
||||
</ul>
|
||||
|
||||
<p><img src="/cgspace-notes/2016/03/url-parameters.png" alt="URL parameters cause millions of dynamic pages" />
|
||||
<img src="/cgspace-notes/2016/03/url-parameters2.png" alt="Setting pages with the filter_0 param not to show in search results" /></p>
|
||||
|
||||
<p><img src="/cgspace-notes/2016/03/url-parameters.png" alt="URL parameters cause millions of dynamic pages">
|
||||
<img src="/cgspace-notes/2016/03/url-parameters2.png" alt="Setting pages with the filter_0 param not to show in search results"></p>
|
||||
<ul>
|
||||
<li>Move AVCD collection to new community and update <code>move_collection.sh</code> script: <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">https://gist.github.com/alanorth/392c4660e8b022d99dfa</a></li>
|
||||
<li>It seems Feedburner can do HTTPS now, so we might be able to update our feeds and simplify the nginx configs</li>
|
||||
<li>De-deploy CGSpace with latest <code>5_x-prod</code> branch</li>
|
||||
<li>Run updates on CGSpace and reboot server (new kernel, <code>4.5.0</code>)</li>
|
||||
<li>Deploy Let’s Encrypt certificate for cgspace.cgiar.org, but still need to work it into the ansible playbooks</li>
|
||||
<li>Deploy Let's Encrypt certificate for cgspace.cgiar.org, but still need to work it into the ansible playbooks</li>
|
||||
</ul>
|
||||
|
||||
<h2 id="2016-03-22">2016-03-22</h2>
|
||||
|
||||
<h2 id="20160322">2016-03-22</h2>
|
||||
<ul>
|
||||
<li>Merge robots.txt patch and disallow indexing of browse pages as our sitemap is consumed correctly (<a href="https://github.com/ilri/DSpace/issues/198">#198</a>)</li>
|
||||
</ul>
|
||||
|
||||
<h2 id="2016-03-23">2016-03-23</h2>
|
||||
|
||||
<h2 id="20160323">2016-03-23</h2>
|
||||
<ul>
|
||||
<li><p>Abenet is having problems saving group memberships, and she gets this error: <a href="https://gist.github.com/alanorth/87281c061c2de57b773e">https://gist.github.com/alanorth/87281c061c2de57b773e</a></p>
|
||||
|
||||
<pre><code>Can't find method org.dspace.app.xmlui.aspect.administrative.FlowGroupUtils.processSaveGroup(org.dspace.core.Context,number,string,[Ljava.lang.String;,[Ljava.lang.String;,org.apache.cocoon.environment.wrapper.RequestWrapper). (resource://aspects/Administrative/administrative.js#967)
|
||||
</code></pre></li>
|
||||
|
||||
<li><p>I can reproduce the same error on DSpace Test and on my Mac</p></li>
|
||||
|
||||
<li><p>Looks to be an issue with the Atmire modules, I’ve submitted a ticket to their tracker.</p></li>
|
||||
<li>Abenet is having problems saving group memberships, and she gets this error: <a href="https://gist.github.com/alanorth/87281c061c2de57b773e">https://gist.github.com/alanorth/87281c061c2de57b773e</a></li>
|
||||
</ul>
|
||||
|
||||
<h2 id="2016-03-24">2016-03-24</h2>
|
||||
|
||||
<pre><code>Can't find method org.dspace.app.xmlui.aspect.administrative.FlowGroupUtils.processSaveGroup(org.dspace.core.Context,number,string,[Ljava.lang.String;,[Ljava.lang.String;,org.apache.cocoon.environment.wrapper.RequestWrapper). (resource://aspects/Administrative/administrative.js#967)
|
||||
</code></pre><ul>
|
||||
<li>I can reproduce the same error on DSpace Test and on my Mac</li>
|
||||
<li>Looks to be an issue with the Atmire modules, I've submitted a ticket to their tracker.</li>
|
||||
</ul>
|
||||
<h2 id="20160324">2016-03-24</h2>
|
||||
<ul>
|
||||
<li>Atmire sent a patch for the group saving issue: <a href="https://github.com/ilri/DSpace/pull/201">https://github.com/ilri/DSpace/pull/201</a></li>
|
||||
<li>I tested it locally and it works, so I merged it to <code>5_x-prod</code> and will deploy on CGSpace this week</li>
|
||||
</ul>
|
||||
|
||||
<h2 id="2016-03-25">2016-03-25</h2>
|
||||
|
||||
<h2 id="20160325">2016-03-25</h2>
|
||||
<ul>
|
||||
<li>Having problems with Listings and Reports, seems to be caused by a rogue reference to <code>dc.type.output</code></li>
|
||||
<li>This is the error we get when we proceed to the second page of Listings and Reports: <a href="https://gist.github.com/alanorth/b2d7fb5b82f94898caaf">https://gist.github.com/alanorth/b2d7fb5b82f94898caaf</a></li>
|
||||
<li>Commenting out the line works, but I haven’t figured out the proper syntax for referring to <code>dc.type.*</code></li>
|
||||
<li>Commenting out the line works, but I haven't figured out the proper syntax for referring to <code>dc.type.*</code></li>
|
||||
</ul>
|
||||
|
||||
<h2 id="2016-03-28">2016-03-28</h2>
|
||||
|
||||
<h2 id="20160328">2016-03-28</h2>
|
||||
<ul>
|
||||
<li>Look into enabling the embargo during item submission, see: <a href="https://wiki.duraspace.org/display/DSDOC5x/Embargo#Embargo-SubmissionProcess">https://wiki.duraspace.org/display/DSDOC5x/Embargo#Embargo-SubmissionProcess</a></li>
|
||||
<li>Seems we only want <code>AccessStep</code> because <code>UploadWithEmbargoStep</code> disables the ability to edit embargos at the item level</li>
|
||||
@ -334,9 +281,7 @@ metadata_value_id | resource_id | metadata_field_id | text_value | text_lang | p
|
||||
<li>This pull request simply updates the config for the dc.type.output → dc.type change that was made last week: <a href="https://github.com/ilri/DSpace/pull/204">https://github.com/ilri/DSpace/pull/204</a></li>
|
||||
<li>Deploy robots.txt fix, embargo for item submissions, and listings and reports fix on CGSpace</li>
|
||||
</ul>
|
||||
|
||||
<h2 id="2016-03-29">2016-03-29</h2>
|
||||
|
||||
<h2 id="20160329">2016-03-29</h2>
|
||||
<ul>
|
||||
<li>Skype meeting with Peter and Addis team to discuss metadata changes for Dublin Core, CGcore, and CGSpace-specific fields</li>
|
||||
<li>We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to <code>cg.*</code>, and then worry about broader changes to DC</li>
|
||||
|
||||
Reference in New Issue
Block a user