cgspace-notes/docs/2019-08/index.html

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Look at Bioversity&rsquo;s latest migration CSV and now I see that Francesco has cleaned up the extra columns and the newline at the end of the file, but many of the column headers have an extra space in the name&hellip;


2019-08-04


Deploy ORCID identifier updates requested by Bioversity to CGSpace
Run system updates on CGSpace (linode18) and reboot it


Before updating it I checked Solr and verified that all statistics cores were loaded properly&hellip;
After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s lucky.

Run system updates on DSpace Test (linode19) and reboot it
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Look at Bioversity&rsquo;s latest migration CSV and now I see that Francesco has cleaned up the extra columns and the newline at the end of the file, but many of the column headers have an extra space in the name&hellip;


2019-08-04


Deploy ORCID identifier updates requested by Bioversity to CGSpace
Run system updates on CGSpace (linode18) and reboot it


Before updating it I checked Solr and verified that all statistics cores were loaded properly&hellip;
After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s lucky.

Run system updates on DSpace Test (linode19) and reboot it
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    <h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-08/">August, 2019</a></h2>
    <p class="blog-post-meta"><time datetime="2019-08-03T12:39:51&#43;03:00">Sat Aug 03, 2019</time> by Alan Orth in 

<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>

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  <h2 id="2019-08-03">2019-08-03</h2>

<ul>
<li>Look at Bioversity&rsquo;s latest migration CSV and now I see that Francesco has cleaned up the extra columns and the newline at the end of the file, but many of the column headers have an extra space in the name&hellip;</li>
</ul>

<h2 id="2019-08-04">2019-08-04</h2>

<ul>
<li>Deploy ORCID identifier updates requested by Bioversity to CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it

<ul>
<li>Before updating it I checked Solr and verified that all statistics cores were loaded properly&hellip;</li>
<li>After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s lucky.</li>
</ul></li>
<li>Run system updates on DSpace Test (linode19) and reboot it</li>
</ul>

<h2 id="2019-08-05">2019-08-05</h2>

<ul>
<li>Update Tomcat to 7.0.96 in the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a></li>
<li>Update PostgreSQL JDBC driver to 42.2.6 in the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastrucutre playbooks</a></li>
<li>Deploy both on DSpace Test (linode19)</li>

<li><p>Looking at the 1429 records for Bioversity migration again</p>

<ul>
<li>The following items use the same exact PDF and seem to be duplicates:</li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=10191">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=10191</a></li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=342">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=342</a></li>
<li>The following items use the same exact PDF, but one seems to be incorrect:</li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=5347">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=5347</a></li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=5340">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=5340</a></li>
<li>The following PDFs are used by several items incorrectly:</li>
<li><code>Report_of_a_Working_Group_on_Allium_7.pdf</code></li>
<li><code>Report_of_a_Working_Group_on_Allium_Fourth_meeting_1696.pdf</code></li>
<li>I checked the SHA1 hashes of each PDF and found that some appear more than once&hellip;</li>
<li>The following items use the same PDF with a different name, but seem to be duplicates (pick one?):</li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=433">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=433</a></li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=10189">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=10189</a></li>
<li>The following items use the same PDF with a different name, but seem to be duplicates (pick one?):</li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=332">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=332</a></li>
<li><a href="https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=10187">https://www.bioversityinternational.org/index.php?id=244&amp;tx_news_pi1[news]=10187</a></li>
<li>There are about thirty PDFs that have French or Spanish filenames and there seems to be an encoding issue</li>
<li>I asked Francesco if he can give me a PDF URL column instead of a &ldquo;filename&rdquo; column so I can download the files myself</li>

<li><p>At <em>least</em> the ~50 filenames identified by the following GREL will have issues:</p>

<pre><code>or(
isNotNull(value.match(/^.*’.*$/)),
isNotNull(value.match(/^.*é.*$/)),
isNotNull(value.match(/^.*á.*$/)),
isNotNull(value.match(/^.*è.*$/)),
isNotNull(value.match(/^.*í.*$/)),
isNotNull(value.match(/^.*ó.*$/)),
isNotNull(value.match(/^.*ú.*$/)),
isNotNull(value.match(/^.*à.*$/)),
isNotNull(value.match(/^.*û.*$/))
).toString()
</code></pre></li>
</ul></li>

<li><p>I tried to extract the filenames and construct a URL to download the PDFs with my <code>generate-thumbnails.py</code> script, but there seem to be several paths for PDFs so I can&rsquo;t guess it properly</p></li>

<li><p>I will have to wait for Francesco to respond about the PDFs, or perhaps proceed with a metadata-only upload so we can do other checks on DSpace Test</p></li>
</ul>

<h2 id="2019-08-06">2019-08-06</h2>

<ul>
<li>Francesca responded to address my feedback yesterday

<ul>
<li>I made some changes to the CSV based on her feedback (remove two duplicates, change one PDF file name, change two titles)</li>
<li>Then I found some items that have PDFs in multiple languages that only list one language in <code>dc.language.iso</code> so I changed them</li>
<li>Strangley, one item was referring to a 7zip file&hellip;</li>
<li>After removing the two duplicates there are now 1427 records</li>
<li>Fix one invalid ISSN: 1020-2002→1020-3362</li>
</ul></li>
</ul>

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<li><a href="/cgspace-notes/2019-08/">August, 2019</a></li>

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