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Working on IFPRI datasets
I noticed the licenses were missing from Nilam&rsquo;s original file so I found a way to check Dataverse&rsquo;s API for a persistent identifier
We have both Handles and DOIs for these datasets, both from Harvard&rsquo;s Dataverse
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Working on IFPRI datasets
I noticed the licenses were missing from Nilam&rsquo;s original file so I found a way to check Dataverse&rsquo;s API for a persistent identifier
We have both Handles and DOIs for these datasets, both from Harvard&rsquo;s Dataverse
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<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/2024-06/">June, 2024</a></h2>
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<time datetime="2024-06-03T14:14:00+03:00">Mon Jun 03, 2024</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2024-06-03">2024-06-03</h2>
<ul>
<li>Working on IFPRI datasets
<ul>
<li>I noticed the licenses were missing from Nilam&rsquo;s original file so I found a way to check <a href="https://guides.dataverse.org/en/latest/api/native-api.html#export-metadata-of-a-dataset-in-various-formats">Dataverse&rsquo;s API for a persistent identifier</a></li>
<li>We have both Handles and DOIs for these datasets, both from Harvard&rsquo;s Dataverse</li>
</ul>
</li>
</ul>
<ul>
<li>I used this GREL in OpenRefine to create a new column based on URLs using the DOI (uppercasing the DOI for Dataverse):</li>
</ul>
<pre tabindex="0"><code>&#34;https://dataverse.harvard.edu/api/datasets/export?exporter=dataverse_json&amp;persistentId=doi:&#34; + value.split(&#39;https://doi.org/&#39;)[-1].toUppercase()
</code></pre><ul>
<li>Then I was able to extract the license text from the JSON response using:</li>
</ul>
<pre tabindex="0"><code>value.parseJson()[&#39;datasetVersion&#39;][&#39;termsOfUse&#39;]
</code></pre><ul>
<li>Similar for the Handle&hellip;</li>
</ul>
<h2 id="2024-06-04">2024-06-04</h2>
<ul>
<li>Some Dataverse entries have the license in <code>['datasetVersion']['license']</code> instead&hellip;</li>
<li>I finalized cleaning the 722 IFPRI datasets and uploaded them to CGSpace</li>
</ul>
<h2 id="2024-06-14">2024-06-14</h2>
<ul>
<li>Minor cleanups on IFPRI&rsquo;s 2016–2019 batch migration file
<ul>
<li>I will start with duplicates on unique identifiers like DOIs</li>
</ul>
</li>
</ul>
<h2 id="2026-06-18">2026-06-18</h2>
<ul>
<li>Merge and upload metadata for duplicates in IFPRI&rsquo;s 2016–2019 set:
<ul>
<li>144 exact match on CGSpace via DOI, type, and date</li>
<li>32 with CGSpace handles</li>
<li>I also spent some time converting the <code>ilri/post_bitstreams.py</code> script to use the DSpace 7 REST API via dspace-rest-client</li>
<li>There are 28 PDFs specified for these 176 duplicates, and a handful of them do not already exist on CGSpace so I will upload them</li>
</ul>
</li>
</ul>
<h2 id="2024-06-19">2024-06-19</h2>
<ul>
<li>Spent some time checking the remaining 3312 IFPRI 2016–2019 migration set for duplicates on CGSpace
<ul>
<li>There seem to be about 50 exact matches of title, type, and issue date</li>
</ul>
</li>
</ul>
<h2 id="2024-06-20">2024-06-20</h2>
<ul>
<li>Finalize merging and uploading metadata for 48 duplicates from the IFPRI 2016–2019 migration set</li>
<li>Heavy load on both CGSpace and DSpace 7 Test this afternoon
<ul>
<li>Took me a while to figure out it was due to someone / something hammering <code>/search</code> for a bunch of facets</li>
<li>The <code>pm2 logs</code> command was more useful than the nginx logs to see the requests at least, for example:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>0|dspace-ui | GET /search?f.sdg=SDG%2013%20-%20Climate%20action,equals&amp;spc.page=1&amp;f.accessRights=Open%20Access,equals&amp;f.dateIssued.min=2023&amp;f.dateIssued.max=2024&amp;f.country=Colombia,equals&amp;f.subject=climate%20change,equals&amp;f.region=Latin%20America%20and%20the%20Caribbean,equals&amp;f.publisher=CGIAR%20FOCUS%20Climate%20Security,equals - - ms - -
1|dspace-ui | GET /search?f.accessRights=Open%20Access,equals&amp;spc.page=1&amp;f.sponsorship=CGIAR%20Trust%20Fund,equals&amp;f.impactArea=Climate%20adaptation%20and%20mitigation,equals&amp;f.region=Eastern%20Africa,equals&amp;f.publisher=International%20Institute%20of%20Tropical%20Agriculture,equals - - ms - -
3|dspace-ui | GET /search?f.sdg=SDG%2013%20-%20Climate%20action,equals&amp;f.sdg=SDG%2012%20-%20Responsible%20consumption%20and%20production,equals&amp;spc.page=1&amp;f.affiliation=CGIAR%20Research%20Program%20on%20Climate%20Change,%20Agriculture%20and%20Food%20Security,equals&amp;f.affiliation=Alliance%20of%20Bioversity%20International%20and%20CIAT,equals&amp;f.dateIssued.min=2020&amp;f.dateIssued.max=2021&amp;f.impactArea=Environmental%20health%20and%20biodiversity,equals - - ms - -
</code></pre><ul>
<li>Still difficult to find the client, because the logs are all <a href="https://github.com/DSpace/dspace-angular/issues/2902">coming from Angular&rsquo;s user agent</a> and IP
<ul>
<li>I changed the nginx logging to use the <code>X-Forwarded-For</code> header, as the default <code>combined</code> log format uses <code>$remote_addr</code> by default, which is only accurate if the request doesn&rsquo;t come from Angular (ie directly to the API)</li>
<li>From what I can see now the IPs are all coming from Huawei Cloud and Tencent</li>
<li>The ASNs are AS136907 (Huawei) and AS132203 (Tencent)</li>
<li>For now I will just add those to the list of bot networks</li>
</ul>
</li>
</ul>
<h2 id="2024-06-21">2024-06-21</h2>
<ul>
<li>Update the nginx logging to use <a href="http://nginx.org/en/docs/http/ngx_http_realip_module.html">nginx&rsquo;s <code>real_ip</code> module</a> to log the correct client IP
<ul>
<li>I think this means we will start sending &lsquo;bot&rsquo; to the Angular / Express frontend because bot IPs will be properly classified now&hellip;</li>
<li>I will have to re-work or at least re-think that nginx configuration for requests going to the frontend because the proposed fix in <a href="https://github.com/DSpace/dspace-angular/issues/2902">https://github.com/DSpace/dspace-angular/issues/2902</a> is to pass on the client&rsquo;s user-agent</li>
</ul>
</li>
<li>Then I updated the list of bot networks:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ wget https://asn.ipinfo.app/api/text/list/AS12876 <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> https://asn.ipinfo.app/api/text/list/AS132203 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS13238 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS136907 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS14061 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS14618 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS16276 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS16509 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS203020 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS204287 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS21859 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS23576 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS24940 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS396982 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS45102 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS50245 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS55286 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS6939 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS8075
</span></span><span style="display:flex;"><span>$ cat AS* | ~/go/bin/mapcidr -a &gt; /tmp/networks.txt
</span></span><span style="display:flex;"><span>$ wc -l /tmp/networks.txt
</span></span><span style="display:flex;"><span>8675 /tmp/networks.txt
</span></span></code></pre></div><ul>
<li>Update list of ORCID identifiers with new ones from Alliance and IFPRI</li>
<li>Finalize uploading the remaining 3,264 items from IFPRI&rsquo;s 2016–2019 batch migration to CGSpace</li>
</ul>
<h2 id="2024-06-24">2024-06-24</h2>
<ul>
<li>Minor updates to <a href="https://github.com/ilri/csv-metadata-quality">csv-metadata-quality</a> and <a href="https://github.com/ilri/cgspace-java-helpers">cgspace-java-helpers</a> to normalize a few more invalid DOI formats</li>
</ul>
<h2 id="2024-06-25">2024-06-25</h2>
<ul>
<li>Work on uploading some missing PDFs from the IFPRI 2016–2019 batch migration</li>
</ul>
<h2 id="2024-06-26">2024-06-26</h2>
<ul>
<li>Did a big cleanup of several thousand journal articles based on metadata from Crossref</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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