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March, 2016 · CGSpace Notes
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<h1><a href="/cgspace-notes/">CGSpace Notes</a></h1>
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<h1 class="text-primary">March, 2016</h1>
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Posted on
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<time datetime="2016-03-02T16:50:00+03:00">
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Mar 2, 2016
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<span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span>
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<h2 id="2016-03-02:5a28ddf3ee658c043c064ccddb151717">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>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="2016-03-07:5a28ddf3ee658c043c064ccddb151717">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>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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<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>
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<h2 id="2016-03-08:5a28ddf3ee658c043c064ccddb151717">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>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="2016-03-10:5a28ddf3ee658c043c064ccddb151717">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>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>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="../images/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="2016-03-11:5a28ddf3ee658c043c064ccddb151717">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 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="2016-03-14:5a28ddf3ee658c043c064ccddb151717">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="../images/2016/03/missing-xmlui-string.png" alt="Missing XMLUI string" /></p>
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<h2 id="2016-03-15:5a28ddf3ee658c043c064ccddb151717">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="2016-03-16:5a28ddf3ee658c043c064ccddb151717">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>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>I noticed that we have some weird values in <code>dc.language</code>:</li>
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</ul>
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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>
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<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="2016-03-17:5a28ddf3ee658c043c064ccddb151717">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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<li>Start discussing CG core with Abenet and Sisay</li>
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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="2016-03-18:5a28ddf3ee658c043c064ccddb151717">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="../images/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="../images/2016/03/bioversity-thumbnail-good.jpg" alt="Trimmed thumbnail" /></p>
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<ul>
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<li>Command used:</li>
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</ul>
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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>
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<ul>
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<li>Also, it looks like adding <code>-sharpen 0x1.0</code> really improves the quality of the image for only a few KB</li>
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</ul>
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<h2 id="2016-03-21:5a28ddf3ee658c043c064ccddb151717">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>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>
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<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>
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<li>I’ve marked them as fixed as well since the ones I tested were working fine</li>
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<li>This raises another question, as many of these pages are linked from Discovery search results and might create a duplicate content problem…</li>
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<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>
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<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>
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<li>For example:
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<ul>
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<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>
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<li>Linked from: <a href="https://cgspace.cgiar.org/jspui/handle/10568/809">https://cgspace.cgiar.org/jspui/handle/10568/809</a></li>
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</ul></li>
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<li>I will mark these errors as resolved because they are returning HTTP 403 on purpose, for a long time!</li>
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<li>Google says the first time it saw this particular error was September 29, 2015… so maybe it accidentally saw it somehow…</li>
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<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>
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</ul>
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<p><img src="../images/2016/03/google-index.png" alt="CGSpace pages in Google index" /></p>
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<ul>
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<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>
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<li>I am not sure if I want to apply it yet</li>
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<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>
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</ul>
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<p><img src="../images/2016/03/url-parameters.png" alt="URL parameters cause millions of dynamic pages" />
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<img src="../images/2016/03/url-parameters2.png" alt="Setting pages with the filter_0 param not to show in search results" /></p>
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<ul>
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<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>
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<li>It seems Feedburner can do HTTPS now, so we might be able to update our feeds and simplify the nginx configs</li>
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<li>De-deploy CGSpace with latest <code>5_x-prod</code> branch</li>
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<li>Run updates on CGSpace and reboot server (new kernel, <code>4.5.0</code>)</li>
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<li>Deploy Let’s Encrypt certificate for cgspace.cgiar.org, but still need to work it into the ansible playbooks</li>
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</ul>
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<h2 id="2016-03-22:5a28ddf3ee658c043c064ccddb151717">2016-03-22</h2>
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<ul>
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<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>
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