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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="May, 2017" />
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<meta property="og:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it's a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire's CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace." />
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<meta property="og:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace." />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-05/" />
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<meta property="article:published_time" content="2017-05-01T16:21:52+02:00" />
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<meta name="twitter:title" content="May, 2017"/>
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<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it's a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire's CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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<link href="https://alanorth.github.io/cgspace-notes/css/style.a20c1a4367639632cdb341d23c27ca44fedcc75b0f8b3cbea6203010da153d3c.css" rel="stylesheet" integrity="sha256-ogwaQ2djljLNs0HSPCfKRP7cx1sPizy+piAwENoVPTw=" crossorigin="anonymous">
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-05/">May, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-05-01T16:21:52+02:00">Mon May 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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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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</ul>
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<h2 id="2017-05-02">2017-05-02</h2>
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<ul>
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<li>Atmire got back about the Workflow Statistics issue, and apparently it's a bug in the CUA module so they will send us a pull request</li>
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<li>Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request</li>
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</ul>
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<h2 id="2017-05-04">2017-05-04</h2>
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<ul>
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<li>Sync DSpace Test with database and assetstore from CGSpace</li>
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<li>Re-deploy DSpace Test with Atmire's CUA patch for workflow statistics, run system updates, and restart the server</li>
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<li>Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server</li>
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<li>Now I can see the workflow statistics and am able to select users, but everything returns 0 items</li>
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<li>Megan says there are still some mapped items are not appearing since last week, so I forced a full <code>index-discovery -b</code></li>
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<li>Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: <a href="https://cgspace.cgiar.org/handle/10568/80731">https://cgspace.cgiar.org/handle/10568/80731</a></li>
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@ -149,8 +149,8 @@
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<li>We decided to use AIP export to preserve the hierarchies and handles of communities and collections</li>
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<li>When ingesting some collections I was getting <code>java.lang.OutOfMemoryError: GC overhead limit exceeded</code>, which can be solved by disabling the GC timeout with <code>-XX:-UseGCOverheadLimit</code></li>
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<li>Other times I was getting an error about heap space, so I kept bumping the RAM allocation by 512MB each time (up to 4096m!) it crashed</li>
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<li>This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using <code>dspace cleanup -v</code>, or else you'll run out of disk space</li>
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<li>In the end I realized it's better to use submission mode (<code>-s</code>) to ingest the community object as a single AIP without its children, followed by each of the collections:</li>
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<li>This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using <code>dspace cleanup -v</code>, or else you’ll run out of disk space</li>
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<li>In the end I realized it’s better to use submission mode (<code>-s</code>) to ingest the community object as a single AIP without its children, followed by each of the collections:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit"
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$ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip
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@ -162,14 +162,14 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<li>Give feedback to CIFOR about their data quality:
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<ul>
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<li>Suggestion: uppercase dc.subject, cg.coverage.region, and cg.coverage.subregion in your crosswalk so they match CGSpace and therefore can be faceted / reported on easier</li>
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<li>Suggestion: use CGSpace's CRP names (cg.contributor.crp), see: dspace/config/input-forms.xml</li>
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<li>Suggestion: use CGSpace’s CRP names (cg.contributor.crp), see: dspace/config/input-forms.xml</li>
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<li>Suggestion: clean up duplicates and errors in funders, perhaps use a controlled vocabulary like ours, see: dspace/config/controlled-vocabularies/dc-description-sponsorship.xml</li>
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<li>Suggestion: use dc.type “Blog Post” instead of “Blog” for your blog post items (we are also adding a “Blog Post” type to CGSpace soon)</li>
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<li>Question: many of your items use dc.document.uri AND cg.identifier.url with the same text value?</li>
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</ul>
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</li>
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<li>Help Marianne from WLE with an Open Search query to show the latest WLE CRP outputs: <a href="https://cgspace.cgiar.org/open-search/discover?query=crpsubject:WATER%2C+LAND+AND+ECOSYSTEMS&sort_by=2&order=DESC">https://cgspace.cgiar.org/open-search/discover?query=crpsubject:WATER%2C+LAND+AND+ECOSYSTEMS&sort_by=2&order=DESC</a></li>
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<li>This uses the webui's item list sort options, see <code>webui.itemlist.sort-option</code> in <code>dspace.cfg</code></li>
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<li>This uses the webui’s item list sort options, see <code>webui.itemlist.sort-option</code> in <code>dspace.cfg</code></li>
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<li>The equivalent Discovery search would be: <a href="https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=WATER%2C+LAND+AND+ECOSYSTEMS&submit_apply_filter=&query=&rpp=10&sort_by=dc.date.issued_dt&order=desc">https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=WATER%2C+LAND+AND+ECOSYSTEMS&submit_apply_filter=&query=&rpp=10&sort_by=dc.date.issued_dt&order=desc</a></li>
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</ul>
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<h2 id="2017-05-09">2017-05-09</h2>
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@ -191,7 +191,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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</ul>
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<h2 id="2017-05-10">2017-05-10</h2>
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<ul>
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<li>Atmire says they are willing to extend the ORCID implementation, and I've asked them to provide a quote</li>
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<li>Atmire says they are willing to extend the ORCID implementation, and I’ve asked them to provide a quote</li>
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<li>I clarified that the scope of the implementation should be that ORCIDs are stored in the database and exposed via REST / API like other fields</li>
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<li>Finally finished importing all the CGIAR Library content, final method was:</li>
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</ul>
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@ -239,7 +239,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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<p>Reboot DSpace Test</p>
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</li>
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<li>
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<p>Fix cron jobs for log management on DSpace Test, as they weren't catching <code>dspace.log.*</code> files correctly and we had over six months of them and they were taking up many gigs of disk space</p>
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<p>Fix cron jobs for log management on DSpace Test, as they weren’t catching <code>dspace.log.*</code> files correctly and we had over six months of them and they were taking up many gigs of disk space</p>
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</li>
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</ul>
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<h2 id="2017-05-16">2017-05-16</h2>
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@ -253,7 +253,7 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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</ul>
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<pre><code>ERROR: duplicate key value violates unique constraint "handle_pkey" Detail: Key (handle_id)=(84834) already exists.
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</code></pre><ul>
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<li>I tried updating the sequences a few times, with Tomcat running and stopped, but it hasn't helped</li>
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<li>I tried updating the sequences a few times, with Tomcat running and stopped, but it hasn’t helped</li>
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<li>It appears item with <code>handle_id</code> 84834 is one of the imported CGIAR Library items:</li>
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</ul>
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<pre><code>dspace=# select * from handle where handle_id=84834;
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@ -269,16 +269,16 @@ $ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager
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86873 | 10947/99 | 2 | 89153
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(1 row)
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</code></pre><ul>
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<li>I've posted on the dspace-test mailing list to see if I can just manually set the <code>handle_seq</code> to that value</li>
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<li>I’ve posted on the dspace-test mailing list to see if I can just manually set the <code>handle_seq</code> to that value</li>
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<li>Actually, it seems I can manually set the handle sequence using:</li>
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</ul>
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<pre><code>dspace=# select setval('handle_seq',86873);
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</code></pre><ul>
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<li>After that I can create collections just fine, though I'm not sure if it has other side effects</li>
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<li>After that I can create collections just fine, though I’m not sure if it has other side effects</li>
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</ul>
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<h2 id="2017-05-21">2017-05-21</h2>
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<ul>
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<li>Start creating a basic theme for the CGIAR System Organization's community on CGSpace</li>
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<li>Start creating a basic theme for the CGIAR System Organization’s community on CGSpace</li>
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<li>Using colors from the <a href="http://library.cgiar.org/handle/10947/2699">CGIAR Branding guidelines (2014)</a></li>
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<li>Make a GitHub issue to track this work: <a href="https://github.com/ilri/DSpace/issues/324">#324</a></li>
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</ul>
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@ -315,14 +315,14 @@ AND resource_id IN (select item_id from collection2item where collection_id IN (
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</code></pre><h2 id="2017-05-23">2017-05-23</h2>
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<ul>
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<li>Add Affiliation to filters on Listing and Reports module (<a href="https://github.com/ilri/DSpace/pull/325">#325</a>)</li>
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<li>Start looking at WLE's Phase II metadata updates but it seems they are not tagging their items properly, as their website importer infers which theme to use based on the name of the CGSpace collection!</li>
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<li>For now I've suggested that they just change the collection names and that we fix their metadata manually afterwards</li>
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<li>Start looking at WLE’s Phase II metadata updates but it seems they are not tagging their items properly, as their website importer infers which theme to use based on the name of the CGSpace collection!</li>
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<li>For now I’ve suggested that they just change the collection names and that we fix their metadata manually afterwards</li>
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<li>Also, they have a lot of messed up values in their <code>cg.subject.wle</code> field so I will clean up some of those first:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_value from metadatavalue where resource_type_id=2 and metadata_field_id=119) to /tmp/wle.csv with csv;
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COPY 111
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</code></pre><ul>
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<li>Respond to Atmire message about ORCIDs, saying that right now we'd prefer to just have them available via REST API like any other metadata field, and that I'm available for a Skype</li>
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<li>Respond to Atmire message about ORCIDs, saying that right now we’d prefer to just have them available via REST API like any other metadata field, and that I’m available for a Skype</li>
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</ul>
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<h2 id="2017-05-26">2017-05-26</h2>
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<ul>
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<li>File an issue on GitHub to explore/track migration to proper country/region codes (ISO 2/3 and UN M.49): <a href="https://github.com/ilri/DSpace/issues/326">#326</a></li>
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<li>Ask Peter how the Landportal.info people should acknowledge us as the source of data on their website</li>
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<li>Communicate with MARLO people about progress on exposing ORCIDs via the REST API, as it is set to be discussed in the <a href="https://wiki.duraspace.org/display/cmtygp/DCAT+Meeting+June+2017">June, 2017 DCAT meeting</a></li>
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<li>Find all of Amos Omore's author name variations so I can link them to his authority entry that has an ORCID:</li>
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<li>Find all of Amos Omore’s author name variations so I can link them to his authority entry that has an ORCID:</li>
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</ul>
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<pre><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Omore, A%';
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</code></pre><ul>
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</ul>
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<pre><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Twine, E%';
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</code></pre><ul>
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<li>But it doesn't look like any of his existing entries are linked to an authority which has an ORCID, so I edited the metadata via “Edit this Item” and looked up his ORCID and linked it there</li>
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<li>But it doesn’t look like any of his existing entries are linked to an authority which has an ORCID, so I edited the metadata via “Edit this Item” and looked up his ORCID and linked it there</li>
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<li>Now I should be able to set his name variations to the new authority:</li>
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</ul>
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<pre><code>dspace=# update metadatavalue set authority='f70d0a01-d562-45b8-bca3-9cf7f249bc8b', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Twine, E%';
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@ -359,7 +359,7 @@ UPDATE 187
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<ul>
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<li>Discuss WLE themes and subjects with Mia and Macaroni Bros</li>
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<li>We decided we need to create metadata fields for Phase I and II themes</li>
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<li>I've updated the existing GitHub issue for Phase II (<a href="https://github.com/ilri/DSpace/issues/322">#322</a>) and created a new one to track the changes for Phase I themes (<a href="https://github.com/ilri/DSpace/issues/327">#327</a>)</li>
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<li>I’ve updated the existing GitHub issue for Phase II (<a href="https://github.com/ilri/DSpace/issues/322">#322</a>) and created a new one to track the changes for Phase I themes (<a href="https://github.com/ilri/DSpace/issues/327">#327</a>)</li>
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<li>After Macaroni Bros update the WLE website importer we will rename the WLE collections to reflect Phase II</li>
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<li>Also, we need to have Mia and Udana look through the existing metadata in <code>cg.subject.wle</code> as it is quite a mess</li>
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</ul>
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