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Add notes for 2021-09-13

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Alan Orth
2021-09-13 16:21:16 +03:00
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@ -50,7 +50,7 @@ DELETE 1
Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)
Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name
"/>
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@ -140,7 +140,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
<ul>
<li>An item was mapped twice erroneously again, so I had to remove one of the mappings manually:</li>
</ul>
<pre><code>dspace=# select * from collection2item where item_id = '80278';
<pre tabindex="0"><code>dspace=# select * from collection2item where item_id = '80278';
id | collection_id | item_id
-------+---------------+---------
92551 | 313 | 80278
@ -166,7 +166,7 @@ DELETE 1
<li>The climate risk management one doesn&rsquo;t exist, so I will have to ask Magdalena if they want me to add it to the input forms</li>
<li>Start testing some nearly 500 author corrections that CCAFS sent me:</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i /tmp/CCAFS-Authors-Feb-7.csv -f dc.contributor.author -t 'correct name' -m 3 -d dspace -u dspace -p fuuu
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/CCAFS-Authors-Feb-7.csv -f dc.contributor.author -t 'correct name' -m 3 -d dspace -u dspace -p fuuu
</code></pre><h2 id="2017-02-09">2017-02-09</h2>
<ul>
<li>More work on CCAFS Phase II stuff</li>
@ -175,7 +175,7 @@ DELETE 1
<li>It&rsquo;s not a very good way to manage the registry, though, as removing one there doesn&rsquo;t cause it to be removed from the registry, and we always restore from database backups so there would never be a scenario when we needed these to be created</li>
<li>Testing some corrections on CCAFS Phase II flagships (<code>cg.subject.ccafs</code>):</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i ccafs-flagships-feb7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i ccafs-flagships-feb7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu
</code></pre><h2 id="2017-02-10">2017-02-10</h2>
<ul>
<li>CCAFS said they want to wait on the flagship updates (<code>cg.subject.ccafs</code>) on CGSpace, perhaps for a month or so</li>
@ -215,46 +215,46 @@ DELETE 1
<li>Fix issue with duplicate declaration of in atmire-dspace-xmlui <code>pom.xml</code> (causing non-fatal warnings during the maven build)</li>
<li>Experiment with making DSpace generate HTTPS handle links, first a change in dspace.cfg or the site&rsquo;s properties file:</li>
</ul>
<pre><code>handle.canonical.prefix = https://hdl.handle.net/
<pre tabindex="0"><code>handle.canonical.prefix = https://hdl.handle.net/
</code></pre><ul>
<li>And then a SQL command to update existing records:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://hdl.handle.net', 'https://hdl.handle.net') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'uri');
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://hdl.handle.net', 'https://hdl.handle.net') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'uri');
UPDATE 58193
</code></pre><ul>
<li>Seems to work fine!</li>
<li>I noticed a few items that have incorrect DOI links (<code>dc.identifier.doi</code>), and after looking in the database I see there are over 100 that are missing the scheme or are just plain wrong:</li>
</ul>
<pre><code>dspace=# select distinct text_value from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value not like 'http%://%';
<pre tabindex="0"><code>dspace=# select distinct text_value from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value not like 'http%://%';
</code></pre><ul>
<li>This will replace any that begin with <code>10.</code> and change them to <code>https://dx.doi.org/10.</code>:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^10\..+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like '10.%';
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^10\..+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like '10.%';
</code></pre><ul>
<li>This will get any that begin with <code>doi:10.</code> and change them to <code>https://dx.doi.org/10.x</code>:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '^doi:(10\..+$)', 'https://dx.doi.org/\1') where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'doi:10%';
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '^doi:(10\..+$)', 'https://dx.doi.org/\1') where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'doi:10%';
</code></pre><ul>
<li>Fix DOIs like <code>dx.doi.org/10.</code> to be <code>https://dx.doi.org/10.</code>:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^dx.doi.org/.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'dx.doi.org/%';
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^dx.doi.org/.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'dx.doi.org/%';
</code></pre><ul>
<li>Fix DOIs like <code>http//</code>:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '^http//(dx.doi.org/.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'http//%';
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '^http//(dx.doi.org/.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'http//%';
</code></pre><ul>
<li>Fix DOIs like <code>dx.doi.org./</code>:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^dx.doi.org\./.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'dx.doi.org./%'
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^dx.doi.org\./.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'dx.doi.org./%'
</code></pre><ul>
<li>Delete some invalid DOIs:</li>
</ul>
<pre><code>dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value in ('DOI','CPWF Mekong','Bulawayo, Zimbabwe','bb');
<pre tabindex="0"><code>dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value in ('DOI','CPWF Mekong','Bulawayo, Zimbabwe','bb');
</code></pre><ul>
<li>Fix some other random outliers:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.1016/j.aquaculture.2015.09.003' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'http:/dx.doi.org/10.1016/j.aquaculture.2015.09.003';
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.1016/j.aquaculture.2015.09.003' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'http:/dx.doi.org/10.1016/j.aquaculture.2015.09.003';
dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.5337/2016.200' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'doi: https://dx.doi.org/10.5337/2016.200';
dspace=# update metadatavalue set text_value = 'https://dx.doi.org/doi:10.1371/journal.pone.0062898' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'Http://dx.doi.org/doi:10.1371/journal.pone.0062898';
dspace=# update metadatavalue set text_value = 'https://dx.doi.10.1016/j.cosust.2013.11.012' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'http:dx.doi.10.1016/j.cosust.2013.11.012';
@ -263,13 +263,13 @@ dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.15446/agro
</code></pre><ul>
<li>And do another round of <code>http://</code> → <code>https://</code> cleanups:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://dx.doi.org', 'https://dx.doi.org') where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'http://dx.doi.org%';
<pre tabindex="0"><code>dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://dx.doi.org', 'https://dx.doi.org') where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'http://dx.doi.org%';
</code></pre><ul>
<li>Run all DOI corrections on CGSpace</li>
<li>Something to think about here is to write a <a href="https://wiki.lyrasis.org/display/DSDOC5x/Curation+System#CurationSystem-ScriptedTasks">Curation Task</a> in Java to do these sanity checks / corrections every night</li>
<li>Then we could add a cron job for them and run them from the command line like:</li>
</ul>
<pre><code>[dspace]/bin/dspace curate -t noop -i 10568/79891
<pre tabindex="0"><code>[dspace]/bin/dspace curate -t noop -i 10568/79891
</code></pre><h2 id="2017-02-20">2017-02-20</h2>
<ul>
<li>Run all system updates on DSpace Test and reboot the server</li>
@ -280,7 +280,7 @@ dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.15446/agro
<li>Testing the <code>fix-metadata-values.py</code> script on macOS and it seems like we don&rsquo;t need to use <code>.encode('utf-8')</code> anymore when printing strings to the screen</li>
<li>It seems this might have only been a temporary problem, as both Python 3.5.2 and 3.6.0 are able to print the problematic string &ldquo;Entwicklung &amp; Ländlicher Raum&rdquo; without the <code>encode()</code> call, but print it as a bytes when it <em>is</em> used:</li>
</ul>
<pre><code>$ python
<pre tabindex="0"><code>$ python
Python 3.6.0 (default, Dec 25 2016, 17:30:53)
&gt;&gt;&gt; print('Entwicklung &amp; Ländlicher Raum')
Entwicklung &amp; Ländlicher Raum
@ -294,7 +294,7 @@ b'Entwicklung &amp; L\xc3\xa4ndlicher Raum'
<li>Testing regenerating PDF thumbnails, like I started in 2016-11</li>
<li>It seems there is a bug in <code>filter-media</code> that causes it to process formats that aren&rsquo;t part of its configuration:</li>
</ul>
<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16856 -p &quot;ImageMagick PDF Thumbnail&quot;
<pre tabindex="0"><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16856 -p &quot;ImageMagick PDF Thumbnail&quot;
File: earlywinproposal_esa_postharvest.pdf.jpg
FILTERED: bitstream 13787 (item: 10568/16881) and created 'earlywinproposal_esa_postharvest.pdf.jpg'
File: postHarvest.jpg.jpg
@ -302,7 +302,7 @@ FILTERED: bitstream 16524 (item: 10568/24655) and created 'postHarvest.jpg.jpg'
</code></pre><ul>
<li>According to <code>dspace.cfg</code> the ImageMagick PDF Thumbnail plugin should only process PDFs:</li>
</ul>
<pre><code>filter.org.dspace.app.mediafilter.ImageMagickImageThumbnailFilter.inputFormats = BMP, GIF, image/png, JPG, TIFF, JPEG, JPEG 2000
<pre tabindex="0"><code>filter.org.dspace.app.mediafilter.ImageMagickImageThumbnailFilter.inputFormats = BMP, GIF, image/png, JPG, TIFF, JPEG, JPEG 2000
filter.org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.inputFormats = Adobe PDF
</code></pre><ul>
<li>I&rsquo;ve sent a message to the mailing list and might file a Jira issue</li>
@ -317,7 +317,7 @@ filter.org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.inputFormats = A
<ul>
<li>Find all fields with &ldquo;<a href="http://hdl.handle.net">http://hdl.handle.net</a>&rdquo; values (most are in <code>dc.identifier.uri</code>, but some are in other URL-related fields like <code>cg.link.reference</code>, <code>cg.identifier.dataurl</code>, and <code>cg.identifier.url</code>):</li>
</ul>
<pre><code>dspace=# select distinct metadata_field_id from metadatavalue where resource_type_id=2 and text_value like 'http://hdl.handle.net%';
<pre tabindex="0"><code>dspace=# select distinct metadata_field_id from metadatavalue where resource_type_id=2 and text_value like 'http://hdl.handle.net%';
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://hdl.handle.net', 'https://hdl.handle.net') where resource_type_id=2 and metadata_field_id IN (25, 113, 179, 219, 220, 223) and text_value like 'http://hdl.handle.net%';
UPDATE 58633
</code></pre><ul>
@ -328,7 +328,7 @@ UPDATE 58633
<ul>
<li>LDAP users cannot log in today, looks to be an issue with CGIAR&rsquo;s LDAP server:</li>
</ul>
<pre><code>$ openssl s_client -connect svcgroot2.cgiarad.org:3269
<pre tabindex="0"><code>$ openssl s_client -connect svcgroot2.cgiarad.org:3269
CONNECTED(00000003)
depth=0 CN = SVCGROOT2.CGIARAD.ORG
verify error:num=20:unable to get local issuer certificate
@ -345,7 +345,7 @@ Certificate chain
<li>For some reason it is now signed by a private certificate authority</li>
<li>This error seems to have started on 2017-02-25:</li>
</ul>
<pre><code>$ grep -c &quot;unable to find valid certification path&quot; [dspace]/log/dspace.log.2017-02-*
<pre tabindex="0"><code>$ grep -c &quot;unable to find valid certification path&quot; [dspace]/log/dspace.log.2017-02-*
[dspace]/log/dspace.log.2017-02-01:0
[dspace]/log/dspace.log.2017-02-02:0
[dspace]/log/dspace.log.2017-02-03:0
@ -381,7 +381,7 @@ Certificate chain
<li>The problem likely lies in the logic of <code>ImageMagickThumbnailFilter.java</code>, as <code>ImageMagickPdfThumbnailFilter.java</code> extends it</li>
<li>Run CIAT corrections on CGSpace</li>
</ul>
<pre><code>dspace=# update metadatavalue set authority='3026b1de-9302-4f3e-85ab-ef48da024eb2', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value = 'International Center for Tropical Agriculture';
<pre tabindex="0"><code>dspace=# update metadatavalue set authority='3026b1de-9302-4f3e-85ab-ef48da024eb2', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value = 'International Center for Tropical Agriculture';
</code></pre><ul>
<li>CGNET has fixed the certificate chain on their LDAP server</li>
<li>Redeploy CGSpace and DSpace Test to on latest <code>5_x-prod</code> branch with fixes for LDAP bind user</li>
@ -393,16 +393,16 @@ Certificate chain
<li>Ah, this is probably because some items have the <code>International Center for Tropical Agriculture</code> author twice, which I first noticed in 2016-12 but couldn&rsquo;t figure out how to fix</li>
<li>I think I can do it by first exporting all metadatavalues that have the author <code>International Center for Tropical Agriculture</code></li>
</ul>
<pre><code>dspace=# \copy (select resource_id, metadata_value_id from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='International Center for Tropical Agriculture') to /tmp/ciat.csv with csv;
<pre tabindex="0"><code>dspace=# \copy (select resource_id, metadata_value_id from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='International Center for Tropical Agriculture') to /tmp/ciat.csv with csv;
COPY 1968
</code></pre><ul>
<li>And then use awk to print the duplicate lines to a separate file:</li>
</ul>
<pre><code>$ awk -F',' 'seen[$1]++' /tmp/ciat.csv &gt; /tmp/ciat-dupes.csv
<pre tabindex="0"><code>$ awk -F',' 'seen[$1]++' /tmp/ciat.csv &gt; /tmp/ciat-dupes.csv
</code></pre><ul>
<li>From that file I can create a list of 279 deletes and put them in a batch script like:</li>
</ul>
<pre><code>delete from metadatavalue where resource_type_id=2 and metadata_field_id=3 and metadata_value_id=2742061;
<pre tabindex="0"><code>delete from metadatavalue where resource_type_id=2 and metadata_field_id=3 and metadata_value_id=2742061;
</code></pre>