<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta property="og:title" content="July, 2017" /> <meta property="og:description" content="2017-07-01 Run system updates and reboot DSpace Test 2017-07-04 Merge changes for WLE Phase II theme rename (#329) Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML: " /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-07/" /> <meta property="article:published_time" content="2017-07-01T18:03:52+03:00"/> <meta property="article:modified_time" content="2018-03-09T22:10:33+02:00"/> <meta name="twitter:card" content="summary"/> <meta name="twitter:title" content="July, 2017"/> <meta name="twitter:description" 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rel="stylesheet" integrity="sha384-CoMzlF7G4xk3ftqRr7leobnWP85AuISUJljMFjtTG/UHyP/+bBwWAvBlXkB4VQQk" crossorigin="anonymous"> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1> <p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-07/">July, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-07-01T18:03:52+03:00">Sat Jul 01, 2017</time> by Alan Orth in <i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a> </p> </header> <h2 id="2017-07-01">2017-07-01</h2> <ul> <li>Run system updates and reboot DSpace Test</li> </ul> <h2 id="2017-07-04">2017-07-04</h2> <ul> <li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li> <li>Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace</li> <li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li> </ul> <p></p> <pre><code>$ psql dspacenew -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=5 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::' </code></pre> <ul> <li>The <code>sed</code> script is from a post on the <a href="https://www.postgresql.org/message-id/437E44A5.508%40ultimeth.com">PostgreSQL mailing list</a></li> <li>Abenet says the ILRI board wants to be able to have “lead author” for every item, so I’ve whipped up a WIP test in the <code>5_x-lead-author</code> branch</li> <li>It works but is still very rough and we haven’t thought out the whole lifecycle yet</li> </ul> <p><img src="/cgspace-notes/2017/07/lead-author-test.png" alt="Testing lead author in submission form" /></p> <ul> <li>I assume that “lead author” would actually be the first question on the item submission form</li> <li>We also need to check to see which ORCID authority core this uses, because it seems to be using an entirely new one rather than the one for <code>dc.contributor.author</code> (which makes sense of course, but fuck, all the author problems aren’t bad enough?!)</li> <li>Also would need to edit XMLUI item displays to incorporate this into authors list</li> <li>And fuck, then anyone consuming our data via REST / OAI will not notice that we have an author outside of <code>dc.contributor.authors</code>… ugh</li> <li>What if we modify the item submission form to use <a href="https://wiki.duraspace.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ItemtypeBasedMetadataCollection"><code>type-bind</code> fields to show/hide certain fields depending on the type</a>?</li> </ul> <h2 id="2017-07-05">2017-07-05</h2> <ul> <li>Adjust WLE Research Theme to include both Phase I and II on the submission form according to editor feedback (<a href="https://github.com/ilri/DSpace/pull/330">#330</a>)</li> <li>Generate list of fields in the current CGSpace <code>cg</code> scheme so we can record them properly in the metadata registry:</li> </ul> <pre><code>$ psql dspace -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=2 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::' > cg-types.xml </code></pre> <ul> <li>CGSpace was unavailable briefly, and I saw this error in the DSpace log file:</li> </ul> <pre><code>2017-07-05 13:05:36,452 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error - org.postgresql.util.PSQLException: FATAL: remaining connection slots are reserved for non-replication superuser connections </code></pre> <ul> <li>Looking at the <code>pg_stat_activity</code> table I saw there were indeed 98 active connections to PostgreSQL, and at this time the limit is 100, so that makes sense</li> <li>Tsega restarted Tomcat and it’s working now</li> <li>Abenet said she was generating a report with Atmire’s CUA module, so it could be due to that?</li> <li>Looking in the logs I see this random error again that I should report to DSpace:</li> </ul> <pre><code>2017-07-05 13:50:07,196 ERROR org.dspace.statistics.SolrLogger @ COUNTRY ERROR: EU </code></pre> <ul> <li>Seems to come from <code>dspace-api/src/main/java/org/dspace/statistics/SolrLogger.java</code></li> </ul> <h2 id="2017-07-06">2017-07-06</h2> <ul> <li>Sisay tried to help by making a <a href="https://github.com/ilri/DSpace/pull/331">pull request for the RTB flagships</a> but there are formatting errors, unrelated changes, and the flagship names are not in the style I requested</li> <li>Abenet talked to CIP and they said they are actually ok with using collection names rather than adding a new metadata field</li> </ul> <h2 id="2017-07-13">2017-07-13</h2> <ul> <li>Remove <code>UKaid</code> from the controlled vocabulary for <code>dc.description.sponsorship</code>, as <code>Department for International Development, United Kingdom</code> is the correct form and it is already present (<a href="https://github.com/ilri/DSpace/pull/334">#334</a>)</li> </ul> <h2 id="2017-07-14">2017-07-14</h2> <ul> <li>Sisay sent me a patch to add “Photo Report” to <code>dc.type</code> so I’ve added it to the <code>5_x-prod</code> branch</li> </ul> <h2 id="2017-07-17">2017-07-17</h2> <ul> <li>Linode shut down our seventeen (17) VMs due to nonpayment of the July 1st invoice</li> <li>It took me a few hours to find the ICT/Finance contacts to pay the bill and boot all the servers back up</li> <li>Since the server was down anyways, I decided to run all system updates and re-deploy CGSpace so that the latest changes to <code>input-forms.xml</code> and the sponsors controlled vocabulary</li> </ul> <h2 id="2017-07-20">2017-07-20</h2> <ul> <li>Skype chat with Addis team about the status of the CGIAR Library migration</li> <li>Need to add the CGIAR System Organization subjects to Discovery Facets (test first)</li> <li>Tentative list of dates for the migration: <ul> <li>August 4: aim to finish data cleanup and then give Peter a list of authors</li> <li>August 18: ready to show System Office</li> <li>September 4: all feedback and decisions (including workflows) from System Office</li> <li>September <sup>10</sup>⁄<sub>11</sub>: go live?</li> </ul></li> <li>Talk to Tsega and Danny about exporting/injesting the blog posts from Drupal into DSpace?</li> <li>Followup meeting on August <sup>8</sup>⁄<sub>9</sub>?</li> <li>Sent Abenet the 2415 records from CGIAR Library’s Historical Archive (<sup>10947</sup>⁄<sub>1</sub>) after cleaning up the author authorities and HTML entities in <code>dc.contributor.author</code> and <code>dc.description.abstract</code> using OpenRefine: <ul> <li>Authors: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></li> <li>Abstracts: <code>replace(value,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')</code></li> </ul></li> </ul> <h2 id="2017-07-24">2017-07-24</h2> <ul> <li>Move two top-level communities to be sub-communities of ILRI Projects</li> </ul> <pre><code>$ for community in 10568/2347 10568/25209; do /home/cgspace.cgiar.org/bin/dspace community-filiator --set --parent=10568/27629 --child="$community"; done </code></pre> <ul> <li>Discuss CGIAR Library data cleanup with Sisay and Abenet</li> </ul> <h2 id="2017-07-27">2017-07-27</h2> <ul> <li>Help Sisay with some transforms to add descriptions to the <code>filename</code> column of some CIAT Presentations he’s working on in OpenRefine</li> <li>Marianne emailed a few days ago to ask why “Integrating Ecosystem Solutions” was not in the list of WLE Phase I Research Themes on the input form</li> <li>I told her that I only added the themes that I saw in the <a href="https://cgspace.cgiar.org/handle/10568/34508">WLE Phase I Research Themes</a> community</li> <li>Then Mia from WLE also emailed to ask where some WLE focal regions went, and I said I didn’t understand what she was talking about, as all we did in our previous work was rename the old “Research Themes” subcommunity to “WLE Phase I Research Themes” and add a new subcommunity for “WLE Phase II Research Themes”.</li> <li>Discuss some modifications to the CCAFS project tags in CGSpace submission form and in the database</li> </ul> <h2 id="2017-07-28">2017-07-28</h2> <ul> <li>Discuss updates to the Phase II CCAFS project tags with Andrea from Macaroni Bros</li> <li>I will do the renaming and untagging of items in CGSpace database, and he will update his webservice with the latest project tags and I will get the XML from here for our <code>input-forms.xml</code>: <a href="https://ccafs.cgiar.org/export/ccafsproject">https://ccafs.cgiar.org/export/ccafsproject</a></li> </ul> <h2 id="2017-07-29">2017-07-29</h2> <ul> <li>Move some WLE items into appropriate Phase I Research Themes communities and delete some empty collections in WLE Regions community</li> </ul> <h2 id="2017-07-30">2017-07-30</h2> <ul> <li>Start working on CCAFS project tag cleanup</li> <li>More questions about inconsistencies and spelling mistakes in their tags, so I’ve sent some questions for followup</li> </ul> <h2 id="2017-07-31">2017-07-31</h2> <ul> <li>Looks like the final list of metadata corrections for CCAFS project tags will be:</li> </ul> <pre><code>delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-FP4_CRMWestAfrica'; update metadatavalue set text_value='FP3_VietnamLED' where resource_type_id=2 and metadata_field_id=134 and text_value='FP3_VeitnamLED'; update metadatavalue set text_value='PII-FP1_PIRCCA' where resource_type_id=2 and metadata_field_id=235 and text_value='PII-SEA_PIRCCA'; delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-WA_IntegratedInterventions'; </code></pre> <ul> <li>Now just waiting to run them on CGSpace, and then apply the modified input forms after Macaroni Bros give me an updated list</li> <li>Temporarily increase the nginx upload limit to 200MB for Sisay to upload the CIAT presentations</li> <li>Looking at CGSpace activity page, there are 52 Baidu bots concurrently crawling our website (I copied the activity page to a text file and grep it)!</li> </ul> <pre><code>$ grep 180.76. /tmp/status | awk '{print $5}' | sort | uniq | wc -l 52 </code></pre> <ul> <li>From looking at the <code>dspace.log</code> I see they are all using the same session, which means our Crawler Session Manager Valve is working</li> </ul> </article> </div> <!-- /.blog-main --> <aside class="col-sm-3 ml-auto blog-sidebar"> <section class="sidebar-module"> <h4>Recent Posts</h4> <ol class="list-unstyled"> <li><a href="/cgspace-notes/2018-04/">April, 2018</a></li> <li><a href="/cgspace-notes/2018-03/">March, 2018</a></li> <li><a href="/cgspace-notes/2018-02/">February, 2018</a></li> <li><a href="/cgspace-notes/2018-01/">January, 2018</a></li> <li><a href="/cgspace-notes/2017-12/">December, 2017</a></li> </ol> </section> <section class="sidebar-module"> <h4>Links</h4> <ol class="list-unstyled"> <li><a href="https://cgspace.cgiar.org">CGSpace</a></li> <li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li> <li><a 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