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Run system updates and reboot DSpace Test
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2017-07-04
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Merge changes for WLE Phase II theme rename (#329)
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Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
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We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
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" />
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<meta name="twitter:title" content="July, 2017"/>
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<meta name="twitter:description" content="2017-07-01
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Run system updates and reboot DSpace Test
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2017-07-04
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Merge changes for WLE Phase II theme rename (#329)
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Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
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We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">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" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-07/">July, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-07-01T18:03:52+03:00">Sat Jul 01, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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</header>
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<h2 id="2017-07-01">2017-07-01</h2>
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<ul>
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<li>Run system updates and reboot DSpace Test</li>
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</ul>
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<h2 id="2017-07-04">2017-07-04</h2>
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<ul>
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<li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li>
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<li>Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace</li>
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<li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
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</ul>
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<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::'
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</code></pre><ul>
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<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>
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<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>
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<li>It works but is still very rough and we haven’t thought out the whole lifecycle yet</li>
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</ul>
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<p><img src="/cgspace-notes/2017/07/lead-author-test.png" alt="Testing lead author in submission form"></p>
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<ul>
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<li>I assume that “lead author” would actually be the first question on the item submission form</li>
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<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>
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<li>Also would need to edit XMLUI item displays to incorporate this into authors list</li>
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<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>
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<li>What if we modify the item submission form to use <a href="https://wiki.lyrasis.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ItemtypeBasedMetadataCollection"><code>type-bind</code> fields to show/hide certain fields depending on the type</a>?</li>
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</ul>
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<h2 id="2017-07-05">2017-07-05</h2>
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<ul>
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<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>
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<li>Generate list of fields in the current CGSpace <code>cg</code> scheme so we can record them properly in the metadata registry:</li>
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</ul>
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<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
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</code></pre><ul>
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<li>CGSpace was unavailable briefly, and I saw this error in the DSpace log file:</li>
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</ul>
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<pre><code>2017-07-05 13:05:36,452 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.postgresql.util.PSQLException: FATAL: remaining connection slots are reserved for non-replication superuser connections
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</code></pre><ul>
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<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>
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<li>Tsega restarted Tomcat and it’s working now</li>
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<li>Abenet said she was generating a report with Atmire’s CUA module, so it could be due to that?</li>
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<li>Looking in the logs I see this random error again that I should report to DSpace:</li>
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</ul>
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<pre><code>2017-07-05 13:50:07,196 ERROR org.dspace.statistics.SolrLogger @ COUNTRY ERROR: EU
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</code></pre><ul>
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<li>Seems to come from <code>dspace-api/src/main/java/org/dspace/statistics/SolrLogger.java</code></li>
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</ul>
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<h2 id="2017-07-06">2017-07-06</h2>
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<ul>
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<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>
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<li>Abenet talked to CIP and they said they are actually ok with using collection names rather than adding a new metadata field</li>
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</ul>
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<h2 id="2017-07-13">2017-07-13</h2>
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<ul>
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<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>
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</ul>
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<h2 id="2017-07-14">2017-07-14</h2>
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<ul>
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<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>
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</ul>
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<h2 id="2017-07-17">2017-07-17</h2>
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<ul>
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<li>Linode shut down our seventeen (17) VMs due to nonpayment of the July 1st invoice</li>
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<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>
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<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>
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</ul>
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<h2 id="2017-07-20">2017-07-20</h2>
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<ul>
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<li>Skype chat with Addis team about the status of the CGIAR Library migration</li>
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<li>Need to add the CGIAR System Organization subjects to Discovery Facets (test first)</li>
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<li>Tentative list of dates for the migration:
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<ul>
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<li>August 4: aim to finish data cleanup and then give Peter a list of authors</li>
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<li>August 18: ready to show System Office</li>
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<li>September 4: all feedback and decisions (including workflows) from System Office</li>
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<li>September 10/11: go live?</li>
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</ul>
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</li>
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<li>Talk to Tsega and Danny about exporting/injesting the blog posts from Drupal into DSpace?</li>
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<li>Followup meeting on August 8/9?</li>
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<li>Sent Abenet the 2415 records from CGIAR Library’s Historical Archive (10947/1) after cleaning up the author authorities and HTML entities in <code>dc.contributor.author</code> and <code>dc.description.abstract</code> using OpenRefine:
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<ul>
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<li>Authors: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></li>
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<li>Abstracts: <code>replace(value,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')</code></li>
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</ul>
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</li>
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</ul>
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<h2 id="2017-07-24">2017-07-24</h2>
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<ul>
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<li>Move two top-level communities to be sub-communities of ILRI Projects</li>
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</ul>
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<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
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</code></pre><ul>
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<li>Discuss CGIAR Library data cleanup with Sisay and Abenet</li>
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</ul>
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<h2 id="2017-07-27">2017-07-27</h2>
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<ul>
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<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>
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<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>
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<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>
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<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>
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<li>Discuss some modifications to the CCAFS project tags in CGSpace submission form and in the database</li>
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</ul>
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<h2 id="2017-07-28">2017-07-28</h2>
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<ul>
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<li>Discuss updates to the Phase II CCAFS project tags with Andrea from Macaroni Bros</li>
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<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>
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</ul>
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<h2 id="2017-07-29">2017-07-29</h2>
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<ul>
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<li>Move some WLE items into appropriate Phase I Research Themes communities and delete some empty collections in WLE Regions community</li>
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</ul>
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<h2 id="2017-07-30">2017-07-30</h2>
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<ul>
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<li>Start working on CCAFS project tag cleanup</li>
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<li>More questions about inconsistencies and spelling mistakes in their tags, so I’ve sent some questions for followup</li>
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</ul>
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<h2 id="2017-07-31">2017-07-31</h2>
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<ul>
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<li>Looks like the final list of metadata corrections for CCAFS project tags will be:</li>
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</ul>
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<pre><code>delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-FP4_CRMWestAfrica';
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update metadatavalue set text_value='FP3_VietnamLED' where resource_type_id=2 and metadata_field_id=134 and text_value='FP3_VeitnamLED';
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update metadatavalue set text_value='PII-FP1_PIRCCA' where resource_type_id=2 and metadata_field_id=235 and text_value='PII-SEA_PIRCCA';
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delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-WA_IntegratedInterventions';
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</code></pre><ul>
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<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>
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<li>Temporarily increase the nginx upload limit to 200MB for Sisay to upload the CIAT presentations</li>
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<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>
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</ul>
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<pre><code>$ grep 180.76. /tmp/status | awk '{print $5}' | sort | uniq | wc -l
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52
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</code></pre><ul>
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<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>
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</ul>
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</article>
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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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/2020-05/">May, 2020</a></li>
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<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
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<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
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</ol>
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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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