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Add notes for 2020-10-19

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Alan Orth
2020-10-19 15:47:59 +03:00
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docs/2019-01/index.html
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@ -26,7 +26,7 @@ I don’t see anything interesting in the web server logs around that time t
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-01/" />
<meta property="article:published_time" content="2019-01-02T09:48:30+02:00" />
<meta property="article:modified_time" content="2019-10-28T13:39:25+02:00" />
<meta property="article:modified_time" content="2020-10-19T15:23:30+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="January, 2019"/>
@ -59,7 +59,7 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
"url": "https://alanorth.github.io/cgspace-notes/2019-01/",
"wordCount": "5532",
"datePublished": "2019-01-02T09:48:30+02:00",
"dateModified": "2019-10-28T13:39:25+02:00",
"dateModified": "2020-10-19T15:23:30+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -791,7 +791,7 @@ sys 0m2.396s
<li>After rebooting I notice that the Linode kernel went down from 4.19.8 to 4.18.16&hellip;</li>
<li>Atmire sent a quote on our <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=657">ticket about purchasing the Metadata Quality Module (MQM) for DSpace 5.8</a></li>
<li>Abenet asked me for an <a href="https://cgspace.cgiar.org/open-search/discover?query=crpsubject:Livestock&amp;sort_by=3&amp;order=DESC">OpenSearch query that could generate and RSS feed for items in the Livestock CRP</a></li>
<li>According to my notes, <code>sort_by=3</code> is accession date (as configured in `dspace.cfg)</li>
<li>According to my notes, <code>sort_by=3</code> is accession date (as configured in <code>dspace.cfg</code>)</li>
<li>The query currently shows 3023 items, but a <a href="https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&amp;filter_relational_operator_1=equals&amp;filter_1=Livestock&amp;submit_apply_filter=&amp;query=">Discovery search for Livestock CRP only returns 858 items</a></li>
<li>That query seems to return items tagged with <code>Livestock and Fish</code> CRP as well&hellip; hmm.</li>
</ul>

184
docs/2020-10/index.html
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@ -23,7 +23,7 @@ During the FlywayDB migration I got an error:
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-10/" />
<meta property="article:published_time" content="2020-10-06T16:55:54+03:00" />
<meta property="article:modified_time" content="2020-10-14T22:21:03+03:00" />
<meta property="article:modified_time" content="2020-10-15T18:11:00+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="October, 2020"/>
@ -51,9 +51,9 @@ During the FlywayDB migration I got an error:
"@type": "BlogPosting",
"headline": "October, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-10/",
"wordCount": "2831",
"wordCount": "3789",
"datePublished": "2020-10-06T16:55:54+03:00",
"dateModified": "2020-10-14T22:21:03+03:00",
"dateModified": "2020-10-15T18:11:00+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -598,6 +598,184 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/dc-subject.x
real 88m21.678s
user 7m59.182s
sys 2m22.713s
</code></pre><h2 id="2020-10-18">2020-10-18</h2>
<ul>
<li>Macaroni Bros wrote to me to ask why some of their CCAFS harvesting is failing
<ul>
<li>They are scraping HTML from /browse responses like this:</li>
</ul>
</li>
</ul>
<p><a href="https://cgspace.cgiar.org/browse?type=crpsubject&amp;value=Climate+Change%2C+Agriculture+and+Food+Security&amp;XML&amp;rpp=5000">https://cgspace.cgiar.org/browse?type=crpsubject&amp;value=Climate+Change%2C+Agriculture+and+Food+Security&amp;XML&amp;rpp=5000</a></p>
<ul>
<li>They are using the user agent &ldquo;CCAFS Website Publications importer BOT&rdquo; so they are getting rate limited by nginx</li>
<li>Ideally they would use the REST <code>find-by-metadata-field</code> endpoint, but it is <em>really</em> slow for large result sets (like twenty minutes!):</li>
</ul>
<pre><code>$ curl -f -H &quot;CCAFS Website Publications importer BOT&quot; -H &quot;Content-Type: application/json&quot; -X POST &quot;https://dspacetest.cgiar.org/rest/items/find-by-metadata-field?limit=100&quot; -d '{&quot;key&quot;:&quot;cg.contributor.crp&quot;, &quot;value&quot;:&quot;Climate Change, Agriculture and Food Security&quot;,&quot;language&quot;: &quot;en_US&quot;}'
</code></pre><ul>
<li>For now I will whitelist their user agent so that they can continue scraping /browse</li>
<li>I figured out that the mappings for AReS are stored in Elasticsearch
<ul>
<li>There is a Kibana interface running on port 5601 that can help explore the values in the index</li>
<li>I can interact with Elasticsearch by sending requests, for example to delete an item by its <code>_id</code>:</li>
</ul>
</li>
</ul>
<pre><code>$ curl -XPOST &quot;localhost:9200/openrxv-values/_delete_by_query&quot; -H 'Content-Type: application/json' -d'
{
&quot;query&quot;: {
&quot;match&quot;: {
&quot;_id&quot;: &quot;64j_THMBiwiQ-PKfCSlI&quot;
}
}
}
</code></pre><ul>
<li>I added a new find/replace:</li>
</ul>
<pre><code>$ curl -XPOST &quot;localhost:9200/openrxv-values/_doc?pretty&quot; -H 'Content-Type: application/json' -d'
{
&quot;find&quot;: &quot;ALAN1&quot;,
&quot;replace&quot;: &quot;ALAN2&quot;,
}
'
</code></pre><ul>
<li>I see it in Kibana, and I can search it in Elasticsearch, but I don&rsquo;t see it in OpenRXV&rsquo;s mapping values dashboard</li>
<li>Now I deleted everything in the <code>openrxv-values</code> index:</li>
</ul>
<pre><code>$ curl -XDELETE http://localhost:9200/openrxv-values
</code></pre><ul>
<li>Then I tried posting it again:</li>
</ul>
<pre><code>$ curl -XPOST &quot;localhost:9200/openrxv-values/_doc?pretty&quot; -H 'Content-Type: application/json' -d'
{
&quot;find&quot;: &quot;ALAN1&quot;,
&quot;replace&quot;: &quot;ALAN2&quot;,
}
'
</code></pre><ul>
<li>But I still don&rsquo;t see it in AReS</li>
<li>Interesting! I added a find/replace manually in AReS and now I see the one I POSTed&hellip;</li>
<li>I fixed a few bugs in the Simple and Extended PDF reports on AReS
<ul>
<li>Add missing ISI Journal and Type to Simple PDF report</li>
<li>Fix DOIs in Simple PDF report</li>
<li>Add missing &ldquo;<a href="https://hdl.handle.net">https://hdl.handle.net</a>&rdquo; to Handles in Extented PDF report</li>
</ul>
</li>
<li>Testing Atmire CUA and L&amp;R based on their feedback from a few days ago
<ul>
<li>I no longer get the NullPointerException from CUA when importing metadata on the command line (!)</li>
<li>Listings and Reports now shows results for simple queries that I tested (!), though it seems that there are some new JavaScript libraries I need to allow in nginx</li>
</ul>
</li>
<li>I sent a mail to the dspace-tech mailing list asking about the error with DSpace 6&rsquo;s &ldquo;Export Search Metadata&rdquo; function
<ul>
<li>If I search for an author like &ldquo;Orth, Alan&rdquo; it gives an HTTP 400, but if I search for &ldquo;Orth&rdquo; alone it exports a CSV</li>
<li>I replicated the same issue on demo.dspace.org</li>
</ul>
</li>
</ul>
<h2 id="2020-10-19">2020-10-19</h2>
<ul>
<li>Last night I learned how to POST mappings to Elasticsearch for AReS:</li>
</ul>
<pre><code>$ curl -XDELETE http://localhost:9200/openrxv-values
$ curl -XPOST http://localhost:9200/openrxv-values/_doc/_bulk -H &quot;Content-Type: application/json&quot; --data-binary @./mapping.json
</code></pre><ul>
<li>The JSON file looks like this, with one instruction on each line:</li>
</ul>
<pre><code>{&quot;index&quot;:{}}
{ &quot;find&quot;: &quot;CRP on Dryland Systems - DS&quot;, &quot;replace&quot;: &quot;Dryland Systems&quot; }
{&quot;index&quot;:{}}
{ &quot;find&quot;: &quot;FISH&quot;, &quot;replace&quot;: &quot;Fish&quot; }
</code></pre><ul>
<li>Adjust the report templates on AReS based on some of Peter&rsquo;s feedback</li>
<li>I wrote a quick Python script to filter and convert the old AReS mappings to <a href="https://www.elastic.co/guide/en/elasticsearch/reference/current/docs-bulk.html">Elasticsearch&rsquo;s Bulk API</a> format:</li>
</ul>
<div class="highlight"><pre 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="color:#75715e">#!/usr/bin/env python3</span>
<span style="color:#f92672">import</span> json
<span style="color:#f92672">import</span> re
f <span style="color:#f92672">=</span> open(<span style="color:#e6db74">&#39;/tmp/mapping.json&#39;</span>, <span style="color:#e6db74">&#39;r&#39;</span>)
data <span style="color:#f92672">=</span> json<span style="color:#f92672">.</span>load(f)
<span style="color:#75715e"># Iterate over old mapping file, which is in format &#34;find&#34;: &#34;replace&#34;, ie:</span>
<span style="color:#75715e">#</span>
<span style="color:#75715e"># &#34;alan&#34;: &#34;ALAN&#34;</span>
<span style="color:#75715e">#</span>
<span style="color:#75715e"># And convert to proper dictionaries for import into Elasticsearch&#39;s Bulk API:</span>
<span style="color:#75715e">#</span>
<span style="color:#75715e"># { &#34;find&#34;: &#34;alan&#34;, &#34;replace&#34;: &#34;ALAN&#34; }</span>
<span style="color:#75715e">#</span>
<span style="color:#66d9ef">for</span> find, replace <span style="color:#f92672">in</span> data<span style="color:#f92672">.</span>items():
<span style="color:#75715e"># Skip all upper and all lower case strings because they are indicative of</span>
<span style="color:#75715e"># some AGROVOC or other mappings we no longer want to do</span>
<span style="color:#66d9ef">if</span> find<span style="color:#f92672">.</span>isupper() <span style="color:#f92672">or</span> find<span style="color:#f92672">.</span>islower() <span style="color:#f92672">or</span> replace<span style="color:#f92672">.</span>isupper() <span style="color:#f92672">or</span> replace<span style="color:#f92672">.</span>islower():
<span style="color:#66d9ef">continue</span>
<span style="color:#75715e"># Skip replacements with acronyms like:</span>
<span style="color:#75715e">#</span>
<span style="color:#75715e"># International Livestock Research Institute - ILRI</span>
<span style="color:#75715e">#</span>
acronym_pattern <span style="color:#f92672">=</span> re<span style="color:#f92672">.</span>compile(<span style="color:#e6db74">r</span><span style="color:#e6db74">&#34;[A-Z]+$&#34;</span>)
acronym_pattern_match <span style="color:#f92672">=</span> acronym_pattern<span style="color:#f92672">.</span>search(replace)
<span style="color:#66d9ef">if</span> acronym_pattern_match <span style="color:#f92672">is</span> <span style="color:#f92672">not</span> None:
<span style="color:#66d9ef">continue</span>
mapping <span style="color:#f92672">=</span> { <span style="color:#e6db74">&#34;find&#34;</span>: find, <span style="color:#e6db74">&#34;replace&#34;</span>: replace }
<span style="color:#75715e"># Print command for Elasticsearch</span>
<span style="color:#66d9ef">print</span>(<span style="color:#e6db74">&#39;{&#34;index&#34;:{}}&#39;</span>)
<span style="color:#66d9ef">print</span>(json<span style="color:#f92672">.</span>dumps(mapping))
f<span style="color:#f92672">.</span>close()
</code></pre></div><ul>
<li>It filters all upper and lower case strings as well as any replacements that end in an acronym like &ldquo;- ILRI&rdquo;, reducing the number of mappings from around 4,000 to about 900</li>
<li>I deleted the existing <code>openrxv-values</code> Elasticsearch core and then POSTed it:</li>
</ul>
<pre><code>$ ./convert-mapping.py &gt; /tmp/elastic-mappings.txt
$ curl -XDELETE http://localhost:9200/openrxv-values
$ curl -XPOST http://localhost:9200/openrxv-values/_doc/_bulk -H &quot;Content-Type: application/json&quot; --data-binary @/tmp/elastic-mappings.txt
</code></pre><ul>
<li>Then in AReS I didn&rsquo;t see the mappings in the dashboard until I added a new one manually, after which they all appeared
<ul>
<li>I started a new harvesting</li>
</ul>
</li>
<li>I checked the CIMMYT DSpace repository and I see they have <a href="https://repository.cimmyt.org/rest">the REST API enabled</a>
<ul>
<li>The data doesn&rsquo;t look too bad actually: they have countries in title case, AGROVOC in upper case, CRPs, etc</li>
<li>According to <a href="https://repository.cimmyt.org/oai/request?verb=ListRecords&amp;metadataPrefix=oai_dc">their OAI</a> they have 6,500 items in the repository</li>
<li>I would be interested to explore the possibility to harvest them&hellip;</li>
</ul>
</li>
<li>Bosede said they were having problems with the &ldquo;Access&rdquo; step during item submission
<ul>
<li>I looked at the Munin graphs for PostgreSQL and both connections and locks look normal so I&rsquo;m not sure what it could be</li>
<li>I restarted the PostgreSQL service just to see if that would help</li>
</ul>
</li>
<li>I ran the <code>dspace cleanup -v</code> process on CGSpace and got an error:</li>
</ul>
<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)=(192921) is still referenced from table &quot;bundle&quot;.
</code></pre><ul>
<li>The solution is, as always:</li>
</ul>
<pre><code>$ psql -d dspace -U dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (192921);'
UPDATE 1
</code></pre><ul>
<li>After looking at the CGSpace Solr stats for 2020-10 I found some hits to purge:</li>
</ul>
<pre><code>$ ./check-spider-hits.sh -f /tmp/agents -s statistics -u http://localhost:8083/solr -p
Purging 2474 hits from ShortLinkTranslate in statistics
Purging 2568 hits from RI\/1\.0 in statistics
Purging 1851 hits from ILRI Livestock Website Publications importer BOT in statistics
Purging 1282 hits from curl in statistics
Total number of bot hits purged: 8174
</code></pre><!-- raw HTML omitted -->

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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
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<meta property="og:updated_time" content="2020-10-19T15:23:30+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>

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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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