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Add notes for 2022-03-04

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Alan Orth
2022-03-04 15:30:06 +03:00
parent 7453499827
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@ -46,7 +46,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# dpkg -C
# reboot
"/>
<meta name="generator" content="Hugo 0.92.2" />
<meta name="generator" content="Hugo 0.93.1" />
@ -153,7 +153,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# tar czf 2019-12-01-linode18-etc.tar.gz /etc
</code></pre><ul>
<li>Then check all third-party repositories in /etc/apt to see if everything using &ldquo;xenial&rdquo; has packages available for &ldquo;bionic&rdquo; and then update the sources:</li>
<li><!-- raw HTML omitted --># sed -i &rsquo;s/xenial/bionic/' /etc/apt/sources.list.d/*.list<!-- raw HTML omitted --></li>
<li><!-- raw HTML omitted --># sed -i &rsquo;s/xenial/bionic/&rsquo; /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>
</ul>
@ -163,7 +163,7 @@ Make sure all packages are up to date and the package manager is up to date, the
<li>After the upgrade finishes, remove Java 11, force the installation of bionic nginx, and reboot the server:</li>
</ul>
<pre tabindex="0"><code># apt purge openjdk-11-jre-headless
# apt install 'nginx=1.16.1-1~bionic'
# apt install &#39;nginx=1.16.1-1~bionic&#39;
# reboot
</code></pre><ul>
<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&rsquo;s working:</li>
@ -195,8 +195,8 @@ Make sure all packages are up to date and the package manager is up to date, the
</ul>
</li>
</ul>
<pre tabindex="0"><code>$ http 'https://cgspace.cgiar.org/oai/request?verb=GetRecord&amp;metadataPrefix=oai_dc&amp;identifier=oai:cgspace.cgiar.org:10568/104030' &gt; /tmp/cgspace-104030.xml
$ http 'https://dspacetest.cgiar.org/oai/request?verb=GetRecord&amp;metadataPrefix=oai_dc&amp;identifier=oai:cgspace.cgiar.org:10568/104030' &gt; /tmp/dspacetest-104030.xml
<pre tabindex="0"><code>$ http &#39;https://cgspace.cgiar.org/oai/request?verb=GetRecord&amp;metadataPrefix=oai_dc&amp;identifier=oai:cgspace.cgiar.org:10568/104030&#39; &gt; /tmp/cgspace-104030.xml
$ http &#39;https://dspacetest.cgiar.org/oai/request?verb=GetRecord&amp;metadataPrefix=oai_dc&amp;identifier=oai:cgspace.cgiar.org:10568/104030&#39; &gt; /tmp/dspacetest-104030.xml
</code></pre><ul>
<li>The DSpace Test ones actually now capture the DOI, where the CGSpace doesn&rsquo;t&hellip;</li>
<li>And the DSpace Test one doesn&rsquo;t include review status as <code>dc.description</code>, but I don&rsquo;t think that&rsquo;s an important field</li>
@ -209,11 +209,11 @@ $ http 'https://dspacetest.cgiar.org/oai/request?verb=GetRecord&amp;metadataPref
</ul>
</li>
</ul>
<pre tabindex="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;
<pre tabindex="0"><code>dspace=# \COPY (SELECT handle, owning_collection FROM item, handle WHERE item.discoverable=&#39;f&#39; AND item.in_archive=&#39;t&#39; AND handle.resource_id = item.item_id) to /tmp/2019-12-04-CGSpace-private-items.csv WITH CSV HEADER;
COPY 48
</code></pre><h2 id="2019-12-05">2019-12-05</h2>
<ul>
<li>Give <a href="https://hdl.handle.net/10568/106045">presentation about CG Core v2</a> to the MEL Developers' Retreat in Nairobi, Kenya (via Skype)</li>
<li>Give <a href="https://hdl.handle.net/10568/106045">presentation about CG Core v2</a> to the MEL Developers&rsquo; Retreat in Nairobi, Kenya (via Skype)</li>
<li>Send some pull requests to the cg-core schema repository:
<ul>
<li><a href="https://github.com/AgriculturalSemantics/cg-core/pull/16">HTML syntax fixes</a></li>
@ -288,14 +288,14 @@ COPY 48
<li>I looked into creating RTF documents from HTML in Node.js and there is a library called <a href="https://www.npmjs.com/package/html-to-rtf">html-to-rtf</a> that works well, but doesn&rsquo;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>
<pre tabindex="0"><code>dspace=# \COPY (SELECT DISTINCT text_value as &quot;dc.contributor.sponsor&quot;, 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;
<pre tabindex="0"><code>dspace=# \COPY (SELECT DISTINCT text_value as &#34;dc.contributor.sponsor&#34;, 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><h2 id="2019-12-18">2019-12-18</h2>
<ul>
<li>Apply the investor corrections and deletions from Peter on CGSpace:</li>
</ul>
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/2019-12-17-investors-fix-112.csv -db dspace -u dspace -p 'fuuu' -f dc.description.sponsorship -m 29 -t correct -d
$ ./delete-metadata-values.py -i /tmp/2019-12-17-investors-delete-68.csv -db dspace -u dspace -p 'fuuu' -m 29 -f dc.description.sponsorship -d
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/2019-12-17-investors-fix-112.csv -db dspace -u dspace -p &#39;fuuu&#39; -f dc.description.sponsorship -m 29 -t correct -d
$ ./delete-metadata-values.py -i /tmp/2019-12-17-investors-delete-68.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 29 -f dc.description.sponsorship -d
</code></pre><ul>
<li>Peter asked about the &ldquo;Open Government Licence 3.0&rdquo; that is used by <a href="">some items</a>
<ul>
@ -304,13 +304,13 @@ $ ./delete-metadata-values.py -i /tmp/2019-12-17-investors-delete-68.csv -db dsp
</ul>
</li>
</ul>
<pre tabindex="0"><code>dspace=# SELECT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=53 AND text_value LIKE '%Open%';
<pre tabindex="0"><code>dspace=# SELECT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=53 AND text_value LIKE &#39;%Open%&#39;;
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%';
dspace=# UPDATE metadatavalue SET text_value=&#39;OGL-UK-3.0&#39; WHERE resource_type_id=2 AND metadata_field_id=53 AND text_value LIKE &#39;%Open Government License 3.0%&#39;;
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 (<a href="https://github.com/ilri/DSpace/pull/440">#440</a>)</li>
@ -338,12 +338,12 @@ UPDATE 2
<ul>
<li>I ran the <code>dspace cleanup</code> process on CGSpace (linode18) and had an error:</li>
</ul>
<pre tabindex="0"><code>Error: ERROR: update or delete on table &quot;bitstream&quot; violates foreign key constraint &quot;bundle_primary_bitstream_id_fkey&quot; on table &quot;bundle&quot;
Detail: Key (bitstream_id)=(179441) is still referenced from table &quot;bundle&quot;.
<pre tabindex="0"><code>Error: ERROR: update or delete on table &#34;bitstream&#34; violates foreign key constraint &#34;bundle_primary_bitstream_id_fkey&#34; on table &#34;bundle&#34;
Detail: Key (bitstream_id)=(179441) is still referenced from table &#34;bundle&#34;.
</code></pre><ul>
<li>The solution is to delete that bitstream manually:</li>
</ul>
<pre tabindex="0"><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (179441);'
<pre tabindex="0"><code>$ psql dspace -c &#39;update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (179441);&#39;
UPDATE 1
</code></pre><ul>
<li>Adjust <a href="/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>