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<meta property="og:description" content="2017-10-01
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Peter emailed to point out that many items in the ILRI archive collection have multiple handles:
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http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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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
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Add Katherine Lutz to the groups for content sumission and edit steps of the CGIAR System collections
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<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="October, 2017"/>
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<meta name="twitter:description" content="2017-10-01
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Peter emailed to point out that many items in the ILRI archive collection have multiple handles:
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http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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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
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Add Katherine Lutz to the groups for content sumission and edit steps of the CGIAR System collections
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<title>October, 2017 | CGSpace Notes</title>
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</header>
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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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<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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</code></pre>
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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 sumission and edit steps of the CGIAR System collections</li>
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</ul>
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<p></p>
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<h2 id="2017-10-02">2017-10-02</h2>
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<ul>
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<li>Peter Ballantyne said he was having problems logging into CGSpace with “both” of his accounts (CGIAR LDAP and personal, apparently)</li>
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<li>I looked in the logs and saw some LDAP lookup failures due to timeout but also strangely a “no DN found” error:</li>
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</ul>
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<pre><code>2017-10-01 20:24:57,928 WARN org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=CA0AA5FEAEA8805645489404CDCE9594:ip_addr=41.204.190.40:ldap_attribute_lookup:type=failed_search javax.naming.CommunicationException\colon; svcgroot2.cgiarad.org\colon;3269 [Root exception is java.net.ConnectException\colon; Connection timed out (Connection timed out)]
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2017-10-01 20:22:37,982 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=CA0AA5FEAEA8805645489404CDCE9594:ip_addr=41.204.190.40:failed_login:no DN found for user pballantyne
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</code></pre>
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<ul>
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<li>I thought maybe his account had expired (seeing as it’s was the first of the month) but he says he was finally able to log in today</li>
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<li>The logs for yesterday show fourteen errors related to LDAP auth failures:</li>
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</ul>
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<pre><code>$ grep -c "ldap_authentication:type=failed_auth" dspace.log.2017-10-01
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14
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</code></pre>
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<ul>
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<li>For what it’s worth, there are no errors on any other recent days, so it must have been some network issue on Linode or CGNET’s LDAP server</li>
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<li>Linode emailed to say that linode578611 (DSpace Test) needs to migrate to a new host for a security update so I initiated the migration immediately rather than waiting for the scheduled time in two weeks</li>
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</ul>
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<h2 id="2017-10-04">2017-10-04</h2>
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<ul>
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<li>Twice in the last twenty-four hours Linode has alerted about high CPU usage on CGSpace (linode2533629)</li>
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<li>Communicate with Sam from the CGIAR System Organization about some broken links coming from their CGIAR Library domain to CGSpace</li>
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<li>The first is a link to a browse page that should be handled better in nginx:</li>
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</ul>
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<pre><code>http://library.cgiar.org/browse?value=Intellectual%20Assets%20Reports&type=subject → https://cgspace.cgiar.org/browse?value=Intellectual%20Assets%20Reports&type=subject
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</code></pre>
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<ul>
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<li>We’ll need to check for browse links and handle them properly, including swapping the <code>subject</code> parameter for <code>systemsubject</code> (which doesn’t exist in Discovery yet, but we’ll need to add it) as we have moved their poorly curated subjects from <code>dc.subject</code> to <code>cg.subject.system</code></li>
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<li>The second link was a direct link to a bitstream which has broken due to the sequence being updated, so I told him he should link to the handle of the item instead</li>
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<li>Help Sisay proof sixty-two IITA records on DSpace Test</li>
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<li>Lots of inconsistencies and errors in subjects, dc.format.extent, regions, countries</li>
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<li>Merge the Discovery search changes for ISI Journal (<a href="https://github.com/ilri/DSpace/pull/341">#341</a>)</li>
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</ul>
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<h2 id="2017-10-05">2017-10-05</h2>
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<ul>
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<li>Twice in the past twenty-four hours Linode has warned that CGSpace’s outbound traffic rate was exceeding the notification threshold</li>
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<li>I had a look at yesterday’s OAI and REST logs in <code>/var/log/nginx</code> but didn’t see anything unusual:</li>
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</ul>
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<pre><code># awk '{print $1}' /var/log/nginx/rest.log.1 | sort -n | uniq -c | sort -h | tail -n 10
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141 157.55.39.240
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145 40.77.167.85
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162 66.249.66.92
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181 66.249.66.95
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211 66.249.66.91
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312 66.249.66.94
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384 66.249.66.90
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1495 50.116.102.77
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3904 70.32.83.92
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9904 45.5.184.196
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# awk '{print $1}' /var/log/nginx/oai.log.1 | sort -n | uniq -c | sort -h | tail -n 10
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5 66.249.66.71
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6 66.249.66.67
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6 68.180.229.31
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8 41.84.227.85
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8 66.249.66.92
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17 66.249.66.65
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24 66.249.66.91
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38 66.249.66.95
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69 66.249.66.90
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148 66.249.66.94
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</code></pre>
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<ul>
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<li>Working on the nginx redirects for CGIAR Library</li>
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<li>We should start using 301 redirects and also allow for <code>/sitemap</code> to work on the library.cgiar.org domain so the CGIAR System Organization people can update their Google Search Console and allow Google to find their content in a structured way</li>
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<li>Remove eleven occurrences of <code>ACP</code> in IITA’s <code>cg.coverage.region</code> using the Atmire batch edit module from Discovery</li>
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<li>Need to investigate how we can verify the library.cgiar.org using the HTML or DNS methods</li>
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<li>Run corrections on 143 ILRI Archive items that had two <code>dc.identifier.uri</code> values (Handle) that Peter had pointed out earlier this week</li>
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<li>I used OpenRefine to isolate them and then fixed and re-imported them into CGSpace</li>
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<li>I manually checked a dozen of them and it appeared that the correct handle was always the second one, so I just deleted the first one</li>
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</ul>
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<h2 id="2017-10-06">2017-10-06</h2>
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<ul>
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<li>I saw a nice tweak to thumbnail presentation on the Cardiff Metropolitan University DSpace: <a href="https://repository.cardiffmet.ac.uk/handle/10369/8780">https://repository.cardiffmet.ac.uk/handle/10369/8780</a></li>
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<li>It adds a subtle border and box shadow, before and after:</li>
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</ul>
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<p><img src="/cgspace-notes/2017/10/dspace-thumbnail-original.png" alt="Original flat thumbnails" />
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<img src="/cgspace-notes/2017/10/dspace-thumbnail-box-shadow.png" alt="Tweaked with border and box shadow" /></p>
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<ul>
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<li>I’ll post it to the Yammer group to see what people think</li>
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<li>I figured out at way to do the HTML verification for Google Search console for library.cgiar.org</li>
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<li>We can drop the HTML file in their XMLUI theme folder and it will get copied to the webapps directory during build/install</li>
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<li>Then we add an nginx alias for that URL in the library.cgiar.org vhost</li>
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<li>This method is kinda a hack but at least we can put all the pieces into git to be reproducible</li>
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<li>I will tell Tunji to send me the verification file</li>
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</ul>
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<h2 id="2017-10-10">2017-10-10</h2>
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<ul>
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<li>Deploy logic to allow verification of the library.cgiar.org domain in the Google Search Console (<a href="https://github.com/ilri/DSpace/pull/343">#343</a>)</li>
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<li>After verifying both the HTTP and HTTPS domains and submitting a sitemap it will be interesting to see how the stats in the console as well as the search results change (currently 28,500 results):</li>
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</ul>
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<p><img src="/cgspace-notes/2017/10/google-search-console.png" alt="Google Search Console" />
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<img src="/cgspace-notes/2017/10/google-search-console-2.png" alt="Google Search Console 2" />
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<img src="/cgspace-notes/2017/10/google-search-results.png" alt="Google Search results" /></p>
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<ul>
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<li>I tried to submit a “Change of Address” request in the Google Search Console but I need to be an owner on CGSpace’s console (currently I’m just a user) in order to do that</li>
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<li>Manually clean up some communities and collections that Peter had requested a few weeks ago</li>
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<li>Delete Community <sup>10568</sup>⁄<sub>102</sub> (ILRI Research and Development Issues)</li>
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<li>Move five collections to <sup>10568</sup>⁄<sub>27629</sub> (ILRI Projects) using <code>move-collections.sh</code> with the following configuration:</li>
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</ul>
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<pre><code>10568/1637 10568/174 10568/27629
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10568/1642 10568/174 10568/27629
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10568/1614 10568/174 10568/27629
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10568/75561 10568/150 10568/27629
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10568/183 10568/230 10568/27629
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</code></pre>
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<ul>
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<li>Delete community <sup>10568</sup>⁄<sub>174</sub> (Sustainable livestock futures)</li>
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<li>Delete collections in <sup>10568</sup>⁄<sub>27629</sub> that have zero items (33 of them!)</li>
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</ul>
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<h2 id="2017-10-11">2017-10-11</h2>
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<ul>
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<li>Peter added me as an owner on the CGSpace property on Google Search Console and I tried to submit a “Change of Address” request for the CGIAR Library but got an error:</li>
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</ul>
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<p><img src="/cgspace-notes/2017/10/search-console-change-address-error.png" alt="Change of Address error" /></p>
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<ul>
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<li>We are sending top-level CGIAR Library traffic to their specific community hierarchy in CGSpace so this type of change of address won’t work—we’ll just need to wait for Google to slowly index everything and take note of the HTTP 301 redirects</li>
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<li>Also the Google Search Console doesn’t work very well with Google Analytics being blocked, so I had to turn off my ad blocker to get the “Change of Address” tool to work!</li>
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</ul>
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<h2 id="2017-10-12">2017-10-12</h2>
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<ul>
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<li>Finally finish (I think) working on the myriad nginx redirects for all the CGIAR Library browse stuff—it ended up getting pretty complicated!</li>
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<li>I still need to commit the DSpace changes (add browse index, XMLUI strings, Discovery index, etc), but I should be able to deploy that on CGSpace soon</li>
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</ul>
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<h2 id="2017-10-14">2017-10-14</h2>
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<ul>
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<li>Run system updates on DSpace Test and reboot server</li>
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<li>Merge changes adding a search/browse index for CGIAR System subject to <code>5_x-prod</code> (<a href="https://github.com/ilri/DSpace/pull/344">#344</a>)</li>
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<li>I checked the top browse links in Google’s search results for <code>site:library.cgiar.org inurl:browse</code> and they are all redirected appropriately by the nginx rewrites I worked on last week</li>
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</ul>
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</article>
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
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<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></li>
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<li><a href="/cgspace-notes/2017-09/">September, 2017</a></li>
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<li><a href="/cgspace-notes/2017-08/">August, 2017</a></li>
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<li><a href="/cgspace-notes/2017-07/">July, 2017</a></li>
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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