<li>Then check all third-party repositories in /etc/apt to see if everything using “xenial” has packages available for “bionic” and then update the sources:</li>
<li><!-- raw HTML omitted --># sed -i ’s/xenial/bionic/’ /etc/apt/sources.list.d/*.list<!-- raw HTML omitted --></li>
<li>Pause the Uptime Robot monitoring for CGSpace</li>
<li>Make sure the update manager is installed and do the upgrade:</li>
<li>After the server comes back up, remove Python virtualenvs that were created with Python 3.5 and re-run certbot to make sure it’s working:</li>
<li>Clear Ansible’s fact cache and re-run the playbooks to update the system’s firewalls, SSH config, etc</li>
<li>Altmetric finally responded to my question about Dublin Core fields
<ul>
<li>They shared a <ahref="https://help.altmetric.com/support/solutions/articles/6000141419-what-metadata-is-required-to-track-our-content-">list of fields they use for tracking</a>, but it only mentions HTML meta tags, and not fields considered when harvesting via OAI</li>
<li>Anyways, there might be some areas we can improve on the HTML meta tags, if I look at one <ahref="https://hdl.handle.net/10568/101623">item with a DOI, ISSN, etc</a> I see that we could at least add status (Open Access) and journal title</li>
<li>I merged a <ahref="https://github.com/ilri/DSpace/pull/438">pull request</a> into the <code>5_x-prod</code> branch to add status and journal title to the XHTML meta tags</li>
</ul>
</li>
</ul>
<h2id="2019-12-02">2019-12-02</h2>
<ul>
<li>Raise the issue of old, low-quality thumbnails with Peter and the CGSpace team
<ul>
<li>I suggested that we move manually uploaded thumbnails from the <code>ORIGINAL</code> bundle to the <code>THUMBNAIL</code> bundle</li>
<li>Also replace old thumbnails where an item is available on Slideshare or YouTube because those are easy to get new, high-quality thumbnails for</li>
</ul>
</li>
<li>Continue testing CG Core v2 implementation on DSpace Test
<ul>
<li>Compare the OAI QDC representation of a few items on CGSpace vs DSpace Test:</li>
<li>The DSpace Test ones actually now capture the DOI, where the CGSpace doesn’t…</li>
<li>And the DSpace Test one doesn’t include review status as <code>dc.description</code>, but I don’t think that’s an important field</li>
</ul>
<h2id="2019-12-04">2019-12-04</h2>
<ul>
<li>Peter noticed that there were about seventy items on CGSpace that were marked as private
<ul>
<li>Some have been withdrawn, but I extracted a list of the forty-eight that were not:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>dspace=# \COPY (SELECT handle, owning_collection FROM item, handle WHERE item.discoverable='f' AND item.in_archive='t' AND handle.resource_id = item.item_id) to /tmp/2019-12-04-CGSpace-private-items.csv WITH CSV HEADER;
COPY 48
</code></pre><h2id="2019-12-05">2019-12-05</h2>
<ul>
<li>Give <ahref="https://hdl.handle.net/10568/106045">presentation about CG Core v2</a> to the MEL Developers’ Retreat in Nairobi, Kenya (via Skype)</li>
<li>Send some pull requests to the cg-core schema repository:
<li><ahref="https://github.com/AgriculturalSemantics/cg-core/pull/18">Build main.css using npm build</a></li>
</ul>
</li>
</ul>
<h2id="2019-12-08">2019-12-08</h2>
<ul>
<li>Enrico noticed that the AReS Explorer on CGSpace (linode18) was down
<ul>
<li>I only see HTTP 502 in the nginx logs on CGSpace… so I assume it’s something wrong with the AReS server</li>
<li>I ran all system updates on the AReS server (linode20) and rebooted it</li>
<li>After rebooting the Explorer was accessible again</li>
</ul>
</li>
</ul>
<h2id="2019-12-09">2019-12-09</h2>
<ul>
<li>Update PostgreSQL JDBC driver to <ahref="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.9">version 42.2.9</a> in <ahref="https://github.com/ilri/rmg-ansible-public">Ansible playbooks</a>
<ul>
<li>Deploy on DSpace Test (linode19) to test before deploying on CGSpace in a few days</li>
</ul>
</li>
<li>Altmetric responded to my question about <ahref="https://hdl.handle.net/10568/97087">the WLE item</a> that has a lower score than its DOI
<ul>
<li>They say that they will “reprocess” the item “before Christmas”</li>
</ul>
</li>
</ul>
<h2id="2019-12-11">2019-12-11</h2>
<ul>
<li>Post <ahref="https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=454830191804416">message to Yammer about good practices for thumbnails on CGSpace</a>
<ul>
<li>On the topic of thumbnails, I’m thinking we might want to force regenerate all PDF thumbnails on CGSpace since we upgraded it to Ubuntu 18.04 and got a new ghostscript…</li>
</ul>
</li>
<li>More discussion about report formats for AReS</li>
<li>Peter noticed that the Atmire reports weren’t showing any statistics before 2019
<ul>
<li>I checked and indeed Solr had an issue loading some core last time it was started</li>
<li>I restarted Tomcat three times before all cores came up successfully</li>
</ul>
</li>
<li>While I was restarting the Tomcat service I upgraded the PostgreSQL JDBC driver to version 42.2.9, which had been deployed on DSpace Test earlier this week</li>
</ul>
<h2id="2019-12-16">2019-12-16</h2>
<ul>
<li>Visit CodeObia office to discuss next phase of OpenRXV/AReS development
<ul>
<li>We discussed using CSV instead of Excel for tabular reports
<ul>
<li>OpenRXV should only have “simple” reports with Dublin Core fields</li>
<li>AReS should have this as well as a customized “extended” report that has CRPs, Subjects, Sponsors, etc from CGSpace</li>
</ul>
</li>
<li>We discussed using RTF instead of Word for graphical reports</li>
</ul>
</li>
</ul>
<h2id="2019-12-17">2019-12-17</h2>
<ul>
<li>Start filing GitHub issues for the reporting features on OpenRXV and AReS
<ul>
<li>I created an issue for the “simple” tabular reports on OpenRXV GitHub (<ahref="https://github.com/ilri/OpenRXV/issues/29">#29</a>)</li>
<li>I created an issue for the “extended” tabular reports on AReS GitHub (<ahref="https://github.com/ilri/AReS/issues/8">#8</a>)</li>
<li>I created an issue for “simple” text reports on the OpenRXV GitHub (<ahref="https://github.com/ilri/OpenRXV/issues/30">#30</a>)</li>
<li>I created an issue for “extended” text reports on the AReS GitHub (<ahref="https://github.com/ilri/AReS/issues/9">#9</a>)</li>
</ul>
</li>
<li>I looked into creating RTF documents from HTML in Node.js and there is a library called <ahref="https://www.npmjs.com/package/html-to-rtf">html-to-rtf</a> that works well, but doesn’t support images</li>
<li>Export a list of all investors (<code>dc.description.sponsorship</code>) for Peter to look through and correct:</li>
</ul>
<pretabindex="0"><code>dspace=# \COPY (SELECT DISTINCT text_value as "dc.contributor.sponsor", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 29 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2019-12-17-investors.csv WITH CSV HEADER;
COPY 643
</code></pre><h2id="2019-12-18">2019-12-18</h2>
<ul>
<li>Apply the investor corrections and deletions from Peter on CGSpace:</li>
<li>Peter asked about the “Open Government Licence 3.0” that is used by <ahref="">some items</a>
<ul>
<li>I notice that it <ahref="https://spdx.org/licenses/OGL-UK-3.0.html">exists in SPDX as <code>UGL-UK-3.0</code></a> so I created a GitHub issue to add this to our controlled vocabulary (<ahref="https://github.com/ilri/DSpace/issues/439">#439</a>)</li>
<li>I only see two in our database that use this for now, so I will update them:</li>
</ul>
</li>
</ul>
<pretabindex="0"><code>dspace=# SELECT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=53 AND text_value LIKE '%Open%';
text_value
-----------------------------
Open Government License 3.0
Open Government License 3.0
(2 rows)
dspace=# UPDATE metadatavalue SET text_value='OGL-UK-3.0' WHERE resource_type_id=2 AND metadata_field_id=53 AND text_value LIKE '%Open Government License 3.0%';
UPDATE 2
</code></pre><ul>
<li>I created a pull request to add the license and merged it to the <code>5_x-prod</code> branch (<ahref="https://github.com/ilri/DSpace/pull/440">#440</a>)</li>
<li>Add three new CCAFS Phase II project tags to CGSpace (<ahref="https://github.com/ilri/DSpace/pull/441">#441</a>)</li>
<li>Linode said DSpace Test (linode19) had an outbound traffic rate of 73Mb/sec for the last two hours
<ul>
<li>I see some Russian bot active in nginx’s access logs:</li>
<li>I see they <em>did</em> check <code>robots.txt</code> and their requests are only going to XMLUI item pages… so I guess I just leave them alone</li>
<li>Peter wrote to ask why this <ahref="https://cgspace.cgiar.org/handle/10568/101286">one WLE item</a> does <ahref="https://api.altmetric.com/v1/handle/10568/101286">not have an Altmetric attention score</a>, but <ahref="https://api.altmetric.com/v1/doi/10.1126/science.aaw0911">the DOI does</a>
<ul>
<li>I tweeted the item just in case, but Peter said that he already did it yesterday</li>
<li>The item was added six months ago…</li>
<li>The DOI has an Altmetric score of 259, but for the Handle it is HTTP 404!</li>
<li>I emailed Altmetric support</li>
</ul>
</li>
</ul>
<h2id="2019-12-22">2019-12-22</h2>
<ul>
<li>I ran the <code>dspace cleanup</code> process on CGSpace (linode18) and had an error:</li>
</ul>
<pretabindex="0"><code>Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
Detail: Key (bitstream_id)=(179441) is still referenced from table "bundle".
</code></pre><ul>
<li>The solution is to delete that bitstream manually:</li>
</ul>
<pretabindex="0"><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (179441);'
UPDATE 1
</code></pre><ul>
<li>Adjust <ahref="/cgspace-notes/cgspace-cgcorev2-migration/">CG Core v2 migrataion notes</a> to use <code>cg.review-status</code> instead of <code>cg.peer-reviewed</code>
<ul>
<li>I had <ahref="https://github.com/AgriculturalSemantics/cg-core/issues/14">raised the issue</a> with Marie-Angelique earlier this month</li>
<li>It makes much more sense to use a wider scope here than a simple boolean</li>
</ul>
</li>
<li>I also noticed another field that we should be using in DCTERMS instead of CG: <code>cg.targetaudience</code>
<ul>
<li><ahref="https://www.dublincore.org/specifications/dublin-core/dcmi-terms/2012-06-14/?v=terms#audience">DCTERMS says that <code>dcterms.audience</code> should be used to describe a A class of entity for whom the resource is intended or useful."</a></li>
<li>I will update my notes for this so that we use that field instead</li>
<li>I don’t see “audience” on the <ahref="https://github.com/AgriculturalSemantics/cg-core/">cg-core</a> repository so I filed <ahref="https://github.com/AgriculturalSemantics/cg-core/issues/19">an issue</a> to raise it with Marie-Angelique</li>
</ul>
</li>
</ul>
<h2id="2019-12-23">2019-12-23</h2>
<ul>
<li>Follow up with Altmetric on the issue where <ahref="https://hdl.handle.net/10568/97087">an item</a> has a different (lower) score for its Handle despite it having a correct DOI (with a higher score)
<ul>
<li>I’ve raised this issue three times to Altmetric this year, and a few weeks ago they said they would re-process the item “before Christmas”</li>
</ul>
</li>
<li>Abenet suggested we use <code>cg.reviewStatus</code> instead of <code>cg.review-status</code> and I agree that we should follow other examples like <code>DCTERMS.accessRights</code> and <code>DCTERMS.isPartOf</code>
<ul>
<li>I updated <ahref="https://github.com/AgriculturalSemantics/cg-core/issues/14">my comment on the cg-core issue on GitHub</a></li>
</ul>
</li>
</ul>
<h2id="2019-12-30">2019-12-30</h2>
<ul>
<li>Altmetric responded a few days ago about the <ahref="https://hdl.handle.net/10568/97087">item</a> that has a different (lower) score for its Handle despite it having a correct DOI (with a higher score)
<ul>
<li>She tweeted the repository link and agreed that it didn’t get picked up by Altmetric</li>
<li>She said she will add this to the existing ticket about the previous items I had raised an issue about</li>
</ul>
</li>
<li>Update Tomcat to version 7.0.99 in the <ahref="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and deploy on DSpace Test (linode19)</li>
