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<p class="lead blog-description" dir="auto">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" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-08/">August, 2022</a></h2>
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<time datetime="2022-08-01T10:22:36+03:00">Mon Aug 01, 2022</time>
in
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2022-08-01">2022-08-01</h2>
<ul>
<li>Our request to add <a href="https://github.com/spdx/license-list-XML/issues/1525">CC-BY-3.0-IGO to SPDX</a> was approved a few weeks ago</li>
</ul>
<h2 id="2022-08-02">2022-08-02</h2>
<ul>
<li>Resume working on the MARLO Innovations
<ul>
<li>Last week Jose had sent me an updated CSV with UTF-8 formatting, which was missing the filename column</li>
<li>I joined it with the older file (stripped down to just the <code>cg.number</code> and <code>filename</code> columns and then did the same cleanups I had done last week</li>
<li>I noticed there are six PDFs unused, so I asked Jose</li>
</ul>
</li>
<li>Spent some time trying to understand the REST API submission issues that Rafael from CIAT is having with tip-approve and tip-submit
<ul>
<li>First, according to my notes in 2020-10, a user must be a <em>collection admin</em> in order to submit via the REST API</li>
<li>Second, a collection must have a “Accept/Reject/Edit Metadata” step defined in the workflow</li>
<li>Also, I referenced my notes from this gist I had made for exactly this purpose! <a href="https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a">https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a</a></li>
</ul>
</li>
</ul>
<h2 id="2022-08-03">2022-08-03</h2>
<ul>
<li>I came up with an interesting idea to add missing countries and AGROVOC terms to the MARLO Innovation metadata
<ul>
<li>I copied the abstract column to two new fields: <code>countrytest</code> and <code>agrovoctest</code> and then used this Jython code as a transform to drop terms that don’t match (using CGSpace’s country list and list of 1,400 AGROVOC terms):</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-python" data-lang="python"><span style="display:flex;"><span><span style="color:#66d9ef">with</span> open(<span style="color:#e6db74">r</span><span style="color:#e6db74">"/tmp/cgspace-countries.txt"</span>,<span style="color:#e6db74">'r'</span>) <span style="color:#66d9ef">as</span> f :
</span></span><span style="display:flex;"><span> countries <span style="color:#f92672">=</span> [name<span style="color:#f92672">.</span>rstrip()<span style="color:#f92672">.</span>lower() <span style="color:#66d9ef">for</span> name <span style="color:#f92672">in</span> f]
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">return</span> <span style="color:#e6db74">"||"</span><span style="color:#f92672">.</span>join([x <span style="color:#66d9ef">for</span> x <span style="color:#f92672">in</span> value<span style="color:#f92672">.</span>split(<span style="color:#e6db74">' '</span>) <span style="color:#66d9ef">if</span> x<span style="color:#f92672">.</span>lower() <span style="color:#f92672">in</span> countries])
</span></span></code></pre></div><ul>
<li>Then I joined them with the other country and AGROVOC columns
<ul>
<li>I had originally tried to use csv-metadata-quality to look up and drop invalid AGROVOC terms but it was timing out ever dozen or so requests</li>
<li>Then I briefly tried to use lightrdf to export a text file of labels from AGROVOC’s RDF, but I couldn’t figure it out</li>
<li>I just realized this will not match countries with spaces in our cell value, ugh… and Jython has weird syntax and errors and I can’t get normal Python code to work here, I’m missing something</li>
</ul>
</li>
<li>Then I extracted the titles, dates, and types and added IDs, then ran them through <code>check-duplicates.py</code> to find the existing items on CGSpace so I can add them as <code>dcterm.relation</code> links</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvcut -l -c dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-08-03-Innovations-Cleaned.csv | sed <span style="color:#e6db74">'1s/line_number/id/'</span> > /tmp/innovations-temp.csv
</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/innovations-temp.csv -u dspacetest -db dspacetest -p <span style="color:#e6db74">'dom@in34sniper'</span> -o /tmp/ccafs-duplicates.csv
</span></span></code></pre></div><ul>
<li>There were about 115 with existing items on CGSpace</li>
<li>Then I did some minor processing and checking of the duplicates file (for example, some titles appear more than once in both files), and joined with the other file (left join):</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvjoin --left -c dc.title ~/Downloads/2022-08-03-Innovations-Cleaned.csv ~/Downloads/2022-08-03-Innovations-relations.csv > /tmp/innovations-with-relations.csv
</span></span></code></pre></div><ul>
<li>Then I used SAFBuilder to create a SimpleItemArchive and import to DSpace Test:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ export JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Dfile.encoding=UTF-8 -Xmx2048m"</span>
</span></span><span style="display:flex;"><span>$ dspace import --add --eperson<span style="color:#f92672">=</span>aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-08-03-innovations.map
</span></span></code></pre></div><ul>
<li>Meeting with Mohammed Salem about harmonizing MEL and CGSpace metadata fields
<ul>
<li>I still need to share our results and recommendations with Peter, Enrico, Sara, Svetlana, et al</li>
</ul>
</li>
<li>I made some minor fixes to csv-metadata-quality while working on the MARLO CRP Innovations</li>
</ul>
<h2 id="2022-08-05">2022-08-05</h2>
<ul>
<li>I discussed issues with the DSpace 7 submission forms on Slack and Mark Wood found that the migration tool creates a non-working submission form
<ul>
<li>After updating the class name of the collection step and removing the “complete” and “sample” steps the submission form was working</li>
<li>Now the issue is that the controlled vocabularies show up like this:</li>
</ul>
</li>
</ul>
<p><img src="/cgspace-notes/2022/08/dspace7-submission.png" alt="Controlled vocabulary bug in DSpace 7"></p>
<ul>
<li>I think we need to add IDs, I will have to check what the implications of that are</li>
<li>Emilio contacted me last week to say they have re-worked their harvester on Hetzner to use a new user agent: <code>AICCRA website harvester</code>
<ul>
<li>I verified that I see it in the REST API logs, but I don’t see any new stats hits for it</li>
<li>I do see 11,000 hits from that IP last month when I had the incorrect nginx configuration that was sending a literal <code>$http_user_agent</code> so I purged those</li>
<li>It is lucky that we have <code>harvest</code> in the DSpace spider agent example file so Solr doesn’t log these hits, nothing needed to be done in nginx</li>
</ul>
</li>
</ul>
<h2 id="2022-08-13">2022-08-13</h2>
<ul>
<li>I noticed there was high load on CGSpace, around 9 or 10
<ul>
<li>Looking at the Munin graphs it seems to just be the last two hours or so, with a slight increase in PostgreSQL connections, firewall traffic, and a more noticeable increase in CPU</li>
<li>DSpace sessions are normal</li>
<li>The number of unique hosts making requests to nginx is pretty low, though it’s only 6AM in the server’s time</li>
</ul>
</li>
<li>I see one IP in Sweden making a lot of requests with a normal user agent: 80.248.237.167
<ul>
<li>This host is on Internet Vikings (INTERNETBOLAGET), and I see 140,000 requests from them in Solr</li>
<li>I see reports of excessive scraping on AbuseIPDB.com</li>
<li>I’m gonna add their 80.248.224.0/20 to the bot-networks.conf in nginx</li>
<li>I will also purge all the hits from this IP in Solr statistics</li>
</ul>
</li>
<li>I also see the core.ac.uk bot making tens of thousands of requests today, but we are already tagging that as a bot in Tomcat’s Crawler Session Manager valve, so they should be sharing a Tomcat session with other bots and not creating too many sessions</li>
</ul>
<h2 id="2022-08-15">2022-08-15</h2>
<ul>
<li>Start indexing on AReS</li>
<li>Add CONSERVATION to ILRI subjects on CGSpace
<ul>
<li>I see that AGROVOC has <code>conservation agriculture</code> and I suggested that we use that instead</li>
</ul>
</li>
</ul>
<h2 id="2022-08-17">2022-08-17</h2>
<ul>
<li>Peter and Jose sent more feedback about the CRP Innovation records from MARLO
<ul>
<li>We expanded the CRP names in the citation and removed the <code>cg.identifier.url</code> URLs because they are ugly and will stop working eventually</li>
<li>The mappings of MARLO links will be done internally with the <code>cg.number</code> IDs like “IN-1119” and the Handle URIs</li>
</ul>
</li>
</ul>
<h2 id="2022-08-18">2022-08-18</h2>
<ul>
<li>I talked to Jose about the CCAFS MARLO records
<ul>
<li>He still hasn’t finished re-processing the PDFs to update the internal MARLO links</li>
<li>I started looking at the other records (MELIAs, OICRs, Policies) and found some minor issues in the MELIAs so I sent feedback to Jose</li>
<li>On second thought, I opened the MELIAs file in OpenRefine and it looks OK, so this must have been a parsing issue in LibreOffice when I was checking the file (or perhaps I didn’t use the correct quoting when importing)</li>
</ul>
</li>
<li>Import the original MELIA v2 CSV file into OpenRefine to fix encoding before processing with csvcut/csvjoin
<ul>
<li>Then extract the IDs and filenames from the original V2 file and join with the UTF-8 file:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvcut -c <span style="color:#e6db74">'cg.number (series/report No.)'</span>,File ~/Downloads/MELIA-Metadata-v2-csv.csv > MELIA-v2-IDs-Files.csv
</span></span><span style="display:flex;"><span>$ csvjoin -c <span style="color:#e6db74">'cg.number (series/report No.)'</span> MELIAs<span style="color:#ae81ff">\ </span>metadata<span style="color:#ae81ff">\ </span>utf8<span style="color:#ae81ff">\ </span>20220816_JM.csv MELIA-v2-IDs-Files.csv > MELIAs-UTF-8-with-files.csv
</span></span></code></pre></div><ul>
<li>Then I imported them into OpenRefine to start metadata cleaning and enrichment</li>
<li>Make some minor changes to <a href="https://github.com/ilri/cgspace-submission-guidelines">cgspace-submission-guidelines</a>
<ul>
<li>Upgrade to Bootstrap v5.2.0</li>
<li>Dedupe value pairs and controlled vocabularies before writing them</li>
<li>Sort the controlled vocabularies before writing them (we don’t do this for value pairs because some are added in specific order, like CRPs)</li>
</ul>
</li>
</ul>
<h2 id="2022-08-19">2022-08-19</h2>
<ul>
<li>Peter Ballantyne sent me metadata for 311 Gender items that need to be duplicate checked on CGSpace before uploading
<ul>
<li>I spent a half an hour in OpenRefine to fix the dates because they only had YYYY, but most abstracts and titles had more specific information about the date</li>
<li>Then I checked for duplicates:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i ~/Downloads/gender-ppts-xlsx.csv -u dspace -db dspace -p <span style="color:#e6db74">'fuuu'</span> -o /tmp/gender-duplicates.csv
</span></span></code></pre></div><ul>
<li>I sent the list of ~130 possible duplicates to Peter to check</li>
<li>Jose sent new versions of the MARLO Innovation/MELIA/OICR/Policy PDFs
<ul>
<li>The idea was to replace tinyurl links pointing to MARLO, but I still see many tinyurl links, some of which point to CGIAR Sharepoint and require a login</li>
<li>I asked them why they don’t just use the original links in the first place in case tinyurl.com disappears</li>
</ul>
</li>
<li>I continued working on the MARLO MELIA v2 UTF-8 metadata
<ul>
<li>I did the same metadata enrichment exercise to extract countries and AGROVOC subjects from the abstract field that I did earlier this month, using a Jython expression to match terms in copies of the abstract field</li>
<li>It helps to replace some characters with spaces first with this GREL: <code>value.replace(/[.\/;(),]/, " ")</code></li>
<li>This caught some extra AGROVOC terms, but unfortunately we only check for single-word terms</li>
<li>Then I checked for existing items on CGSpace matching these MELIA using my duplicate checker:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i ~/Downloads/2022-08-18-MELIAs-UTF-8-With-Files.csv -u dspace -db dspace -p <span style="color:#e6db74">'fuuu'</span> -o /tmp/melia-matches.csv
</span></span></code></pre></div><ul>
<li>Then I did some minor processing and checking of the duplicates file (for example, some titles appear more than once in both files), and joined with the other file (left join):</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ xsv join --left id ~/Downloads/2022-08-18-MELIAs-UTF-8-With-Files.csv id ~/Downloads/melia-matches-csv.csv > /tmp/melias-with-relations.csv
</span></span></code></pre></div><ul>
<li>I had to use <code>xsv</code> because <code>csvcut</code> was throwing an error detecting the dialect of the input CSVs (?)</li>
<li>I created a SAF bundle and imported the 749 MELIAs to DSpace Test</li>
<li>I found thirteen items on CGSpace with dates in format “DD/MM/YYYY” so I fixed those</li>
</ul>
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<li><a href="/cgspace-notes/2022-08/">August, 2022</a></li>
<li><a href="/cgspace-notes/2022-07/">July, 2022</a></li>
<li><a href="/cgspace-notes/2022-06/">June, 2022</a></li>
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