<li>Follow up with Carol and Francesca from Bioversity as they were on holiday during the mid-to-late August
<ul>
<li>I told them to check the <ahref="https://dspacetest.cgiar.org/handle/10568/103999">temporary collection on DSpace Test</a> where I uploaded the 1,427 items so they can see how it will look</li>
<li>Also, I told them to advise me about the strange file extensions (.7z, .zip, .lck)</li>
<li>Also, I reminded Abenet to check the metadata, as the institutional authors at least will need some modification</li>
<li>It looks like these items were uploaded by Sisay on 2018-12-19 so we can use the <ahref="https://cgspace.cgiar.org/handle/10568/68616/discover?filtertype_1=dateAccessioned&filter_relational_operator_1=contains&filter_1=2018-12-19&submit_apply_filter=&query=">accession date as a filter</a> to narrow it down to 230 items (of which only 104 have PDFs, according to the Daniel1807.xls input input file)</li>
<li>Now I just checked a few manually and they are correct in the original input file, so something must have happened when Sisay was processing them for upload</li>
<li>Continue working on CG Core v2 migration, focusing on the crosswalk mappings
<ul>
<li>I think we can skip the MODS crosswalk for now because it is only used in <ahref="https://wiki.duraspace.org/display/DSDOC5x/DSpace+AIP+Format#DSpaceAIPFormat-MODSSchema">AIP exports that are meant for non-DSpace systems</a></li>
<li>We should probably do the QDC crosswalk as well as those in <code>xhtml-head-item.properties</code>…</li>
<li>Ouch, there is potentially a lot of work in the OAI metadata formats like DIM, METS, and QDC (see <code>dspace/config/crosswalks/oai/*.xsl</code>)</li>
<li>In general I think I should only modify the left side of the crosswalk mappings (ie, where metadata is coming from) so we maintain the same exact output for search engines, etc</li>
<li>Maria Garruccio asked me to add two new Bioversity ORCID identifiers to CGSpace so I created a <ahref="https://github.com/ilri/DSpace/pull/431">pull request</a></li>
<li>Marissa Van Epp asked me to add new CCAFS Phase II project tags to CGSpace so I created a <ahref="https://github.com/ilri/DSpace/pull/432">pull request</a>
<ul>
<li>I will wait until I hear from her to merge it because there is one tag that seems to be a duplicate because its name (PII-WA_agrosylvopast) is similar to one that already exists (PII-WA_AgroSylvopastoralSystems)</li>
</ul></li>
<li>More work on the CG Core v2 migrations
<ul>
<li>I have updated my <ahref="https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409">notes on the possible changes</a> and done more work on the XMLUI replacements</li>
</ul></li>
</ul>
<h2id="2019-09-12">2019-09-12</h2>
<ul>
<li>Deploy <ahref="https://jdbc.postgresql.org/">PostgreSQL JDBC driver</a> version 42.2.7 on DSpace Test and update the <ahref="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a></li>
<li>Deploy Bioversity ORCID identifier updates to CGSpace</li>
<li>Deploy PostgreSQL JDBC driver 42.2.7 on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and restart the server
<ul>
<li>After restarting the system Tomcat came back up, but not all Solr statistics cores were loaded</li>
<li>I had to restart Tomcat one more time until the cores were loaded (verified in the Solr admin)</li>
</ul></li>
<li>Update nginx TLS cipher suite to the latest <ahref="https://ssl-config.mozilla.org/#server=nginx&server-version=1.16.1&config=intermediate&openssl-version=1.0.2g">Mozilla intermediate recommendations for nginx 1.16.0 and openssl 1.0.2</a>
<ul>
<li>DSpace Test (linode19) is running Ubuntu 18.04 with nginx 1.17.x and openssl 1.1.1 so it can even use TLS v1.3 if we override the nginx ssl protocol in its host vars</li>
</ul></li>
<li><p>XMLUI item view pages are blank on CGSpace right now</p>
<ul>
<li><p>Like earliert this year, I see the following error in the Cocoon log while browsing:</p>
<pre><code>2019-09-15 15:32:18,137 WARN org.apache.cocoon.components.xslt.TraxErrorListener - Can not load requested doc: unknown protocol: cocoon at jndi:/localhost/themes/CIAT/xsl/../../0_CGIAR/xsl//aspect/artifactbrowser/common.xsl:141:90
</code></pre></li>
</ul></li>
<li><p>Around the same time I see the following in the DSpace log:</p>
<pre><code>2019-09-15 15:32:18,079 INFO org.dspace.usage.LoggerUsageEventListener @ aorth@blah:session_id=A11C362A7127004C24E77198AF9E4418:ip_addr=x.x.x.x:view_item:handle=10568/103644
2019-09-15 15:32:18,135 WARN org.dspace.core.PluginManager @ Cannot find named plugin for interface=org.dspace.content.crosswalk.DisseminationCrosswalk, name="METSRIGHTS"
</code></pre></li>
<li><p>I see a lot of these errors today, but not earlier this month:</p>
<pre><code># grep -c 'Cannot find named plugin' dspace.log.2019-09-*
dspace.log.2019-09-01:0
dspace.log.2019-09-02:0
dspace.log.2019-09-03:0
dspace.log.2019-09-04:0
dspace.log.2019-09-05:0
dspace.log.2019-09-06:0
dspace.log.2019-09-07:0
dspace.log.2019-09-08:0
dspace.log.2019-09-09:0
dspace.log.2019-09-10:0
dspace.log.2019-09-11:0
dspace.log.2019-09-12:0
dspace.log.2019-09-13:0
dspace.log.2019-09-14:0
dspace.log.2019-09-15:808
</code></pre></li>
<li><p>Something must have happened when I restarted Tomcat a few hours ago, because earlier in the DSpace log I see a bunch of errors like this:</p>
<pre><code>2019-09-15 13:59:24,136 ERROR org.dspace.core.PluginManager @ Name collision in named plugin, implementation class="org.dspace.content.crosswalk.METSRightsCrosswalk", name="METSRIGHTS"
2019-09-15 13:59:24,136 ERROR org.dspace.core.PluginManager @ Name collision in named plugin, implementation class="org.dspace.content.crosswalk.OREDisseminationCrosswalk", name="ore"
2019-09-15 13:59:24,136 ERROR org.dspace.core.PluginManager @ Name collision in named plugin, implementation class="org.dspace.content.crosswalk.DIMDisseminationCrosswalk", name="dim"
</code></pre></li>
<li><p>I restarted Tomcat and the item views came back, but then the Solr statistics cores didn’t all load properly</p>
<ul>
<li>After restarting Tomcat once again, both the item views and the Solr statistics cores all came back OK</li>
<li><p>In my test environment this added 390 ORCID identifier</p></li>
<li><p>I ran the same updates on CGSpace and DSpace Test and then started a Discovery re-index to force the search index to update</p></li>
<li><p>Update the PostgreSQL JDBC driver to version 42.2.8 in our <ahref="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a></p>
<ul>
<li>There is only <ahref="https://github.com/pgjdbc/pgjdbc/issues/1567">one minor fix to a usecase we aren’t using</a> so I will deploy this on the servers the next time I do updates</li>
</ul></li>
<li><p>Run system updates on DSpace Test (linode19) and reboot it</p></li>
<li><p>Start looking at IITA’s latest round of batch updates that Sisay had <ahref="https://dspacetest.cgiar.org/handle/10568/105486">uploaded to DSpace Test</a> earlier this month</p>
<ul>
<li>For posterity, IITA’s original input file was 20196th.xls and Sisay uploaded it as “IITA_Sep_06” to DSpace Test</li>
<li>Sisay said he did ran the csv-metadata-quality script on the records, but I assume he didn’t run the unsafe fixes or AGROVOC checks because I still see unneccessary Unicode, excessive whitespace, one invalid ISBN, missing dates and a few invalid AGROVOC fields</li>
<li>In addition, a few records were missing authorship type</li>
<li>I deleted two invalid AGROVOC terms because they were ambiguous</li>
<li>Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:</li>
<li><code>$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id</code></li>
<li>I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colum and populate it using this GREL: <code>if(cell.recon.matched, cell.recon.match.name, value)</code></li>
<li>I also looked through the IITA subjects to normalize some values</li>
</ul></li>
<li><p>Follow up with Marissa again about the CCAFS phase II project tags</p></li>
<li><p>Generate a list of the top 1500 authors on CGSpace:</p>
<pre><code>dspace=# \copy (SELECT DISTINCT text_value, 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 LIMIT 1500) to /tmp/2019-09-19-top-1500-authors.csv WITH CSV HEADER;
</code></pre></li>
<li><p>Then I used <code>csvcut</code> to select the column of author names, strip the header and quote characters, and saved the sorted file:</p>
<li>Skype with Carol and Francesca to discuss the Bioveristy migration to CGSpace
<ul>
<li>They want to do some enrichment of the metadata to add countries and regions</li>
<li>Also, they noticed that some items have a blank ISSN in the citation like “ISSN:”</li>
<li>I told them it’s probably best if we have Francesco produce a new export from Typo 3</li>
<li>Note to self that I will need to go apply some of my edits to the resulting file once we get it:</li>
<li>Remove duplicates and rename originals according to Francesca’s feedback (see “RE: Bioversity to CGSpace publications migration” from August 6, 2019)</li>
<li>Unzip zip and 7z files to attach original PDFs if possible (and update filename column)</li>
