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Create an &ldquo;AfricaRice books and book chapters&rdquo; collection on CGSpace for AfricaRice
Last month Sisay asked why the following &ldquo;most popular&rdquo; statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
DSpace Test
CGSpace
Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
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Create an &ldquo;AfricaRice books and book chapters&rdquo; collection on CGSpace for AfricaRice
Last month Sisay asked why the following &ldquo;most popular&rdquo; statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
DSpace Test
CGSpace
Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description">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"><a href="https://alanorth.github.io/cgspace-notes/2019-07/">July, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-07-01T12:13:51&#43;03:00">Mon Jul 01, 2019</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
<h2 id="2019-07-01">2019-07-01</h2>
<ul>
<li>Create an &ldquo;AfricaRice books and book chapters&rdquo; collection on CGSpace for AfricaRice</li>
<li>Last month Sisay asked why the following &ldquo;most popular&rdquo; statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
<ul>
<li><a href="https://dspacetest.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">DSpace Test</a></li>
<li><a href="https://cgspace.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">CGSpace</a></li>
</ul></li>
<li>Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community</li>
</ul>
<ul>
<li>If I change the parameters to 2019 I see stats, so I&rsquo;m really thinking it has something to do with the sharded yearly Solr statistics cores
<ul>
<li>I checked the Solr admin UI and I see all Solr cores loaded, so I don&rsquo;t know what it could be</li>
<li>When I check the Atmire content and usage module it seems obvious that there is a problem with the old cores because I dont have anything before 2019-01</li>
</ul></li>
</ul>
<p><img src="/cgspace-notes/2019/07/atmire-cua-2018-missing.png" alt="Atmire CUA 2018 stats missing" /></p>
<ul>
<li>I don&rsquo;t see anyone logged in right now so I&rsquo;m going to try to restart Tomcat and see if the stats are accessible after Solr comes back up</li>
<li><p>I decided to run all system updates on the server (linode18) and reboot it</p>
<ul>
<li>After rebooting Tomcat came back up, but the the Solr statistics cores were not all loaded</li>
<li><p>The error is always (with a different core):</p>
<pre><code>org.apache.solr.common.SolrException: Error CREATEing SolrCore 'statistics-2010': Unable to create core [statistics-2010] Caused by: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2010/data/index/write.lock
</code></pre></li>
</ul></li>
<li><p>I restarted Tomcat <em>ten times</em> and it never worked&hellip;</p></li>
<li><p>I tried to stop Tomcat and delete the write locks:</p>
<pre><code># systemctl stop tomcat7
# find /dspace/solr/statistics* -iname &quot;*.lock&quot; -print -delete
/dspace/solr/statistics/data/index/write.lock
/dspace/solr/statistics-2010/data/index/write.lock
/dspace/solr/statistics-2011/data/index/write.lock
/dspace/solr/statistics-2012/data/index/write.lock
/dspace/solr/statistics-2013/data/index/write.lock
/dspace/solr/statistics-2014/data/index/write.lock
/dspace/solr/statistics-2015/data/index/write.lock
/dspace/solr/statistics-2016/data/index/write.lock
/dspace/solr/statistics-2017/data/index/write.lock
/dspace/solr/statistics-2018/data/index/write.lock
# find /dspace/solr/statistics* -iname &quot;*.lock&quot; -print -delete
# systemctl start tomcat7
</code></pre></li>
<li><p>But it still didn&rsquo;t work!</p></li>
<li><p>I stopped Tomcat, deleted the old locks, and will try to use the &ldquo;simple&rdquo; lock file type in <code>solr/statistics/conf/solrconfig.xml</code>:</p>
<pre><code>&lt;lockType&gt;${solr.lock.type:simple}&lt;/lockType&gt;
</code></pre></li>
<li><p>And after restarting Tomcat it still doesn&rsquo;t work</p></li>
<li><p>Now I&rsquo;ll try going back to &ldquo;native&rdquo; locking with <code>unlockAtStartup</code>:</p>
<pre><code>&lt;unlockOnStartup&gt;true&lt;/unlockOnStartup&gt;
</code></pre></li>
<li><p>Now the cores seem to load, but I still see an error in the Solr Admin UI and I still can&rsquo;t access any stats before 2018</p></li>
<li><p>I filed an <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685">issue with Atmire</a>, so let&rsquo;s see if they can help</p></li>
<li><p>And since I&rsquo;m annoyed and it&rsquo;s been a few months, I&rsquo;m going to move the JVM heap settings that I&rsquo;ve been testing on DSpace Test to CGSpace</p></li>
<li><p>The old ones were:</p>
<pre><code>-Djava.awt.headless=true -Xms8192m -Xmx8192m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=5400 -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false
</code></pre></li>
<li><p>And the new ones come from Solr 4.10.x&rsquo;s startup scripts:</p>
<pre><code>-Djava.awt.headless=true
-Xms8192m -Xmx8192m
-Dfile.encoding=UTF-8
-XX:NewRatio=3
-XX:SurvivorRatio=4
-XX:TargetSurvivorRatio=90
-XX:MaxTenuringThreshold=8
-XX:+UseConcMarkSweepGC
-XX:+UseParNewGC
-XX:ConcGCThreads=4 -XX:ParallelGCThreads=4
-XX:+CMSScavengeBeforeRemark
-XX:PretenureSizeThreshold=64m
-XX:+UseCMSInitiatingOccupancyOnly
-XX:CMSInitiatingOccupancyFraction=50
-XX:CMSMaxAbortablePrecleanTime=6000
-XX:+CMSParallelRemarkEnabled
-XX:+ParallelRefProcEnabled
-Dcom.sun.management.jmxremote
-Dcom.sun.management.jmxremote.port=1337
-Dcom.sun.management.jmxremote.ssl=false
-Dcom.sun.management.jmxremote.authenticate=false
</code></pre></li>
</ul>
<h2 id="2019-07-02">2019-07-02</h2>
<ul>
<li><p>Help upload twenty-seven posters from the 2019-05 Sharefair to CGSpace</p>
<ul>
<li><p>Sisay had already done the SAFBundle so I did some minor corrections to and uploaded them to a temporary collection so I could check them in OpenRefine:</p>
<pre><code>$ sed -i 's/CC-BY 4.0/CC-BY-4.0/' item_*/dublin_core.xml
$ echo &quot;10568/101992&quot; &gt;&gt; item_*/collections
$ dspace import -a -e me@cgiar.org -m 2019-07-02-Sharefair.map -s /tmp/Sharefair_mapped
</code></pre></li>
</ul></li>
<li><p>I noticed that all twenty-seven items had double dates like &ldquo;2019-05||2019-05&rdquo; so I fixed those, but the rest of the metadata looked good so I unmapped them from the temporary collection</p></li>
<li><p>Finish looking at the fifty-six AfricaRice items and upload them to CGSpace:</p>
<pre><code>$ dspace import -a -e me@cgiar.org -m 2019-07-02-AfricaRice-11to73.map -s /tmp/SimpleArchiveFormat
</code></pre></li>
<li><p>Peter pointed out that the Sharefair dates I fixed were not actually fixed</p>
<ul>
<li>It seems there is a bug that causes DSpace to not detect changes if the values are the same like &ldquo;2019-05||2019-05&rdquo; and you try to remove one</li>
<li>To get it to work I had to change some of them to 2019-01, then remove them</li>
</ul></li>
</ul>
<h2 id="2019-07-03">2019-07-03</h2>
<ul>
<li>Atmire responded about the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685">Solr issue</a> and said they would be willing to help</li>
</ul>
<h2 id="2019-07-04">2019-07-04</h2>
<ul>
<li><p>Maria Garruccio sent me some new ORCID identifiers for Bioversity authors</p>
<ul>
<li><p>I combined them with our existing list and then used my <code>resolve-orcids.py</code> script to update the names from ORCID.org:</p>
<pre><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/new-bioversity-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u &gt; /tmp/2019-07-04-orcid-ids.txt
$ ./resolve-orcids.py -i /tmp/2019-07-04-orcid-ids.txt -o 2019-07-04-orcid-names.txt -d
</code></pre></li>
</ul></li>
<li><p>Send and merge a pull request for the new ORCID identifiers (<a href="https://github.com/ilri/DSpace/pull/428">#428</a>)</p></li>
<li><p>I created a CSV with some ORCID identifiers that I had seen change so I could update any existing ones in the databse:</p>
<pre><code>cg.creator.id,correct
&quot;Marius Ekué: 0000-0002-5829-6321&quot;,&quot;Marius R.M. Ekué: 0000-0002-5829-6321&quot;
&quot;Mwungu: 0000-0001-6181-8445&quot;,&quot;Chris Miyinzi Mwungu: 0000-0001-6181-8445&quot;
&quot;Mwungu: 0000-0003-1658-287X&quot;,&quot;Chris Miyinzi Mwungu: 0000-0003-1658-287X&quot;
</code></pre></li>
<li><p>But when I ran <code>fix-metadata-values.py</code> I didn&rsquo;t see any changes:</p>
<pre><code>$ ./fix-metadata-values.py -i 2019-07-04-update-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -m 240 -t correct -d
</code></pre></li>
</ul>
<h2 id="2019-07-06">2019-07-06</h2>
<ul>
<li>Send a reminder to Marie about my notes on the <a href="https://github.com/AgriculturalSemantics/cg-core/issues/2">CG Core v2 issue I created two weeks ago</a></li>
</ul>
<h2 id="2019-07-08">2019-07-08</h2>
<ul>
<li>Communicate with Atmire about the Solr statistics cores issue
<ul>
<li>I suspect we might need to get more disk space on DSpace Test so we can try to replicate the production environment more closely</li>
</ul></li>
<li>Meeting with AgroKnow and CTA about their new ICT Update story telling thing
<ul>
<li>AgroKnow has developed a React application to display tag clouds based on harvesting metadata and full text from CGSpace items</li>
<li>We discussed how to host it technically, perhaps we purchase a server to run it on and just give AgroKnow guys access</li>
</ul></li>
<li><p>Playing with the idea of using <a href="https://github.com/BurntSushi/xsv">xsv</a> to do some basic batch quality checks on CSVs, for example to find items that might be duplicates if they have the same DOI or title:</p>
<pre><code>$ xsv frequency --select cg.identifier.doi --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E ',1'
field,value,count
cg.identifier.doi,https://doi.org/10.1016/j.agwat.2018.06.018,2
$ xsv frequency --select dc.title --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E ',1'
field,value,count
dc.title,Reference evapotranspiration prediction using hybridized fuzzy model with firefly algorithm: Regional case study in Burkina Faso,2
</code></pre></li>
<li><p>Or perhaps if DOIs are valid or not (having doi.org in the URL):</p>
<pre><code>$ xsv frequency --select cg.identifier.doi --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E 'doi.org'
field,value,count
cg.identifier.doi,https://hdl.handle.net/10520/EJC-1236ac700f,1
</code></pre></li>
<li><p>Or perhaps items with invalid ISSNs (according to the <a href="https://en.wikipedia.org/wiki/International_Standard_Serial_Number#Code_format">ISSN code format</a>):</p>
<pre><code>$ xsv select dc.identifier.issn cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v '&quot;' | grep -v -E '^[0-9]{4}-[0-9]{3}[0-9xX]$'
dc.identifier.issn
978-3-319-71997-9
978-3-319-71997-9
978-3-319-71997-9
978-3-319-58789-9
2320-7035
2593-9173
</code></pre></li>
</ul>
<h2 id="2019-07-09">2019-07-09</h2>
<ul>
<li>Thinking about data cleaning automation again and found some resources about Python and Pandas:
<ul>
<li><a href="https://realpython.com/python-data-cleaning-numpy-pandas/">https://realpython.com/python-data-cleaning-numpy-pandas/</a></li>
<li><a href="https://mode.com/blog/python-data-cleaning-libraries">https://mode.com/blog/python-data-cleaning-libraries</a></li>
</ul></li>
</ul>
<h2 id="2019-07-11">2019-07-11</h2>
<ul>
<li>Skype call with Marie Angelique about CG Core v2
<ul>
<li>We discussed my comments and suggestions from last week</li>
<li>One comment she had was that we should try to move our center-specific subjects into <code>DCTERMS.subject</code> and normalize them against AGROVOC</li>
<li>I updated my <a href="https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409">gist about CGSpace metadata changes</a></li>
</ul></li>
<li>Skype call with Jane Poole to discuss OpenRXV/AReS Phase II TORs
<ul>
<li>I need to follow up with Moayad about the reporting functionality</li>
<li>Also, I need to email Harrison my notes on the CG Core v2 stuff</li>
<li>Also, Jane asked me to check the Data Portal to see which email address requests for confidential data are going</li>
</ul></li>
<li>Yesterday Theirry from CTA asked me about an error he was getting while submitting an item on CGSpace: &ldquo;Unable to load Submission Information, since WorkspaceID (ID:S106658) is not a valid in-process submission.&rdquo;</li>
<li><p>I looked in the DSpace logs and found this right around the time of the screenshot he sent me:</p>
<pre><code>2019-07-10 11:50:27,433 INFO org.dspace.submit.step.CompleteStep @ lewyllie@cta.int:session_id=A920730003BCAECE8A3B31DCDE11A97E:submission_complete:Completed submission with id=106658
</code></pre></li>
<li><p>I&rsquo;m assuming something happened in his browser (like a refresh) after the item was submitted&hellip;</p></li>
</ul>
<h2 id="2019-07-12">2019-07-12</h2>
<ul>
<li>Atmire responded with some initial feedback about our Tomcat configuration related to the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685">Solr issue I raised recently</a>
<ul>
<li>Unfortunately there is no concrete feedback yet</li>
<li>I think we need to upgrade our DSpace Test server so we can fit all the Solr cores&hellip;</li>
<li>Actually, I looked and there were over 40 GB free on DSpace Test so I copied the Solr statistics cores for the years 2017 to 2010 from CGSpace to DSpace Test because they weren&rsquo;t actually very large</li>
<li>I re-deployed DSpace for good measure, and I think all Solr cores are loading&hellip; I will do more tests later</li>
</ul></li>
<li>Run all system updates on DSpace Test (linode19) and reboot it</li>
<li><p>Try to run <code>dspace cleanup -v</code> on CGSpace and ran into an error:</p>
<pre><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)=(167394) is still referenced from table &quot;bundle&quot;.
</code></pre></li>
<li><p>The solution is, as always:</p>
<pre><code># su - postgres
$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (167394);'
UPDATE 1
</code></pre></li>
</ul>
<h2 id="2019-07-16">2019-07-16</h2>
<ul>
<li><p>Completely reset the Podman configuration on my laptop because there were some layers that I couldn&rsquo;t delete and it had been some time since I did a cleanup:</p>
<pre><code>$ podman system prune -a -f --volumes
$ sudo rm -rf ~/.local/share/containers
</code></pre></li>
<li><p>Then pull a new PostgreSQL 9.6 image and load a CGSpace database dump into a new local test container:</p>
<pre><code>$ podman pull postgres:9.6-alpine
$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
$ createuser -h localhost -U postgres --pwprompt dspacetest
$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost ~/Downloads/cgspace_2019-07-16.backup
$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
</code></pre></li>
<li><p>Start working on implementing the <a href="https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409">CG Core v2 changes</a> on my local DSpace test environment</p></li>
<li><p>Make a pull request to CG Core v2 with some fixes for typos in the specification (<a href="https://github.com/AgriculturalSemantics/cg-core/pull/5">#5</a>)</p></li>
</ul>
<h2 id="2019-07-18">2019-07-18</h2>
<ul>
<li>Talk to Moayad about the remaining issues for OpenRXV / AReS
<ul>
<li>He sent a pull request with some changes for the bar chart and documentation about configuration, and said he&rsquo;d finish the export feature next week</li>
</ul></li>
<li><p>Sisay said a user was having problems registering on CGSpace and it looks like the email account expired again:</p>
<pre><code>$ dspace test-email
About to send test email:
- To: blahh@cgiar.org
- Subject: DSpace test email
- Server: smtp.office365.com
Error sending email:
- Error: javax.mail.AuthenticationFailedException
Please see the DSpace documentation for assistance.
</code></pre></li>
<li><p>I emailed ICT to ask them to reset it and make the expiration period longer if possible</p></li>
</ul>
<h2 id="2019-07-19">2019-07-19</h2>
<ul>
<li>ICT reset the password for the CGSpace support account and apparently removed the expiry requirement
<ul>
<li>I tested the account and it&rsquo;s working</li>
</ul></li>
</ul>
<h2 id="2019-07-20">2019-07-20</h2>
<ul>
<li><p>Create an account for Lionelle Samnick on CGSpace because the registration isn&rsquo;t working for some reason:</p>
<pre><code>$ dspace user --add --givenname Lionelle --surname Samnick --email blah@blah.com --password 'blah'
</code></pre></li>
<li><p>I added her as a submitter to <a href="https://cgspace.cgiar.org/handle/10568/74536">CTA ISF Pro-Agro series</a></p></li>
<li><p>Start looking at 1429 records for the Bioversity batch import</p>
<ul>
<li>Multiple authors should be specified with multi-value separatator (||) instead of ;</li>
<li>We don&rsquo;t use &ldquo;(eds)&rdquo; as an author</li>
<li>Same issue with dc.publisher using &ldquo;;&rdquo; for multiple values</li>
<li>Some invalid ISSNs in dc.identifier.issn (they look like ISBNs)</li>
<li>I see some ISSNs in the dc.identifier.isbn field</li>
<li>I see some invalid ISBNs that look like Excel errors (9,78E+12)</li>
<li>For DOI we just use the URL, not &ldquo;DOI: <a href="https://doi.org...&quot;">https://doi.org...&quot;</a></li>
<li>I see an invalid &ldquo;LEAVE BLANK&rdquo; in the cg.contributor.crp field</li>
<li>Country field is using &ldquo;,&rdquo; for multiple values instead of &ldquo;||&rdquo;</li>
<li>Region field is using &ldquo;,&rdquo; for multiple values instead of &ldquo;||&rdquo;</li>
<li>Language field should be lowercase like &ldquo;en&rdquo;, and it is using the wrong multiple value separator, and has some invalid values</li>
<li>What is the cg.identifier.url2 field? You should probably add those as cg.link.reference</li>
</ul></li>
</ul>
<h2 id="2019-07-22">2019-07-22</h2>
<ul>
<li><p>Raise an <a href="https://github.com/AgriculturalSemantics/cg-core/issues/8">issue on CG Core v2 spec regarding country and region coverage</a></p>
<ul>
<li><p>The current standard has them implemented as a class like this:</p>
<pre><code>&lt;dct:coverage&gt;
&lt;dct:spatial&gt;
&lt;type&gt;Country&lt;/type&gt;
&lt;dct:identifier&gt;http://sws.geonames.org/192950&lt;/dct:identifier&gt;
&lt;rdfs:label&gt;Kenya&lt;/rdfs:label&gt;
&lt;/dct:spatial&gt;
&lt;/dct:coverage&gt;
</code></pre></li>
</ul></li>
<li><p>I left a note saying that DSpace is technically limited to a flat schema so we use <code>cg.coverage.country: Kenya</code></p></li>
<li><p>Do a little more work on CG Core v2 in the input forms</p></li>
</ul>
<h2 id="2019-07-25">2019-07-25</h2>
<ul>
<li>Generate a list of the ORCID identifiers that we added to CGSpace in 2019 for Sara Jani at ICARDA</li>
<li><p>Bioversity sent a new file for their migration to CGSpace</p>
<ul>
<li>There is always a blank row and blank column at the end</li>
<li>One invalid type (Brie)</li>
<li>824 items with leading/trailing spaces in dc.identifier.citation</li>
<li>175 items with a trailing comma in dc.identifier.citation (using custom text facet with GREL <code>value.endsWith(',').toString()</code>)</li>
<li>Fix them with GREL transform: <code>value.replace(/,$/, '')</code></li>
<li>A few strange publishers after splitting multi-value cells, like &ldquo;(Belgium)&rdquo;</li>
<li>Deleted four ISSNs that are actually ISBNs and are already present in the ISBN field</li>
<li>Eight invalid ISBNs</li>
<li>Convert all DOIs to &ldquo;<a href="https://doi.org&quot;">https://doi.org&quot;</a> format and fix one invalid DOI</li>
<li>Fix a handful of incorrect CRPs that seem to have been split on comma &ldquo;,&rdquo;</li>
<li>Lots of strange values in cg.link.reference, and I normalized all DOIs to <a href="https://doi.org">https://doi.org</a> format</li>
<li>There are lots of invalid links here, like &ldquo;36&rdquo; and &ldquo;recordlink:publications:2606&rdquo; and &ldquo;t3://record?identifier=publications&amp;uid=2606&rdquo;</li>
<li>Also there are hundreds of items that use the same value for cg.link.reference AND cg.link.dataurl</li>
<li>Use https:// for all Bioversity links (reference, data url, permalink)</li>
</ul></li>
<li><p>I might be able to use <a href="https://pypi.org/project/isbnlib/">isbnlib</a> to validate ISBNs in Python:</p>
<pre><code>if isbnlib.is_isbn10('9966-955-07-0') or isbnlib.is_isbn13('9966-955-07-0'):
print(&quot;Yes&quot;)
else:
print(&quot;No&quot;)
</code></pre></li>
<li><p>Or with <a href="https://github.com/arthurdejong/python-stdnum">python-stdnum</a>:</p>
<pre><code>from stdnum import isbn
from stdnum import issn
isbn.validate('978-92-9043-389-7')
issn.validate('1020-3362')
</code></pre></li>
</ul>
<h2 id="2019-07-26">2019-07-26</h2>
<ul>
<li><p>Bioversity sent me an updated CSV file that fixes some of the issues I pointed out yesterday</p>
<ul>
<li>There are still 1429 records</li>
<li>There are still one extra row and one extra column</li>
<li>There are still eight invalid ISBNs (according to my <code>validate.py</code> script)</li>
</ul></li>
<li><p>I figured out a GREL to trim spaces in multi-value cells without splitting them:</p>
<pre><code>value.replace(/\s+\|\|/,&quot;||&quot;).replace(/\|\|\s+/,&quot;||&quot;)
</code></pre></li>
<li><p>I whipped up a quick script using Python Pandas to do whitespace cleanup</p></li>
</ul>
<h2 id="2019-07-29">2019-07-29</h2>
<ul>
<li>I turned the Pandas script into a proper Python package called <a href="https://git.sr.ht/~alanorth/csv-metadata-quality">csv-metadata-quality</a>
<ul>
<li>It supports CSV and Excel files</li>
<li>It fixes whitespace errors and erroneous multi-value separators (&ldquo;|&rdquo;) and validates ISSN, ISBNs, and dates</li>
<li>Also I added a bunch of other checks/fixes for unnecessary and &ldquo;suspicious&rdquo; Unicode characters</li>
</ul></li>
<li>Inform Bioversity that there is an error in their CSV, seemingly caused by quotes in the citation field</li>
</ul>
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