Add notes for 2022-09-16

2024-11-22 14:45:03 +01:00 · 2022-09-16 17:09:32 +03:00 · 2022-09-16 17:09:32 +03:00 · 1b15837e4e
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@ -231,4 +231,10 @@ COMMIT
 - Meeting with Peter, Abenet, Indira, and Michael about CGSpace rollout plan for the Initiatives
 ## 2022-09-16
 - Meeting with Marie-Angeqlique, Abenet, Margarita, and Sara about types for CG Core
  - We are about halfway through the list of types now, with concrete actions for CG Core and CGSpace
  - We will meet next in two weeks to hopefully finalize the list, then we can move on to definitions
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 A bit of work on the &ldquo;Mapping CG Core–CGSpace–MEL–MARLO Types&rdquo; spreadsheet
 I tested an item submission on DSpace Test with the Cocoon org.apache.cocoon.uploads.autosave=false change
 The submission works as expected
 Start debugging some region-related issues with csv-metadata-quality
 I created a new test file test-geography.csv with some different scenarios
 I also fixed a few bugs and improved the region-matching logic
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 A bit of work on the &ldquo;Mapping CG Core–CGSpace–MEL–MARLO Types&rdquo; spreadsheet
 I tested an item submission on DSpace Test with the Cocoon org.apache.cocoon.uploads.autosave=false change
 The submission works as expected
 Start debugging some region-related issues with csv-metadata-quality
 I created a new test file test-geography.csv with some different scenarios
 I also fixed a few bugs and improved the region-matching logic
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 <time datetime="2022-09-01T09:41:36+03:00">Thu Sep 01, 2022</time>
 in 
 <span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
 </p>
  </header>
  <h2 id="2022-09-01">2022-09-01</h2>
 <ul>
 <li>A bit of work on the &ldquo;Mapping CG Core–CGSpace–MEL–MARLO Types&rdquo; spreadsheet</li>
 <li>I tested an item submission on DSpace Test with the Cocoon <code>org.apache.cocoon.uploads.autosave=false</code> change
 <ul>
 <li>The submission works as expected</li>
 </ul>
 </li>
 <li>Start debugging some region-related issues with csv-metadata-quality
 <ul>
 <li>I created a new test file <code>test-geography.csv</code> with some different scenarios</li>
 <li>I also fixed a few bugs and improved the region-matching logic</li>
 </ul>
 </li>
 </ul>
 <ul>
 <li>I filed <a href="https://github.com/konstantinstadler/country_converter/issues/115">an issue for the &ldquo;South-eastern Asia&rdquo; case mismatch in country_converter</a> on GitHub</li>
 <li>Meeting with Moayad to discuss OpenRXV developments
 <ul>
 <li>He demoed his new multiple dashboards feature and I helped him rebase those changes to master so we can test them more</li>
 </ul>
 </li>
 </ul>
 <h2 id="2022-09-02">2022-09-02</h2>
 <ul>
 <li>I worked a bit more on exclusion and skipping logic in csv-metadata-quality
 <ul>
 <li>I also pruned and updated all the Python dependencies</li>
 <li>Then I released <a href="https://github.com/ilri/csv-metadata-quality/releases/tag/v0.6.0">version 0.6.0</a> now that the excludes and region matching support is working way better</li>
 </ul>
 </li>
 </ul>
 <h2 id="2022-09-05">2022-09-05</h2>
 <ul>
 <li>Started a harvest on AReS last night</li>
 <li>Looking over the Solr statistics from last month I see many user agents that look suspicious:
 <ul>
 <li>Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.2; WOW64; Trident/7.0; .NET4.0E; .NET4.0C)</li>
 <li>Mozilla / 5.0(Windows NT 10.0; Win64; x64) AppleWebKit / 537.36(KHTML, like Gecko) Chrome / 77.0.3865.90 Safari / 537.36</li>
 <li>Mozilla/5.0 (Windows NT 10.0; WOW64; Rv:50.0) Gecko/20100101 Firefox/50.0</li>
 <li>Mozilla/5.0 (X11; Linux i686; rv:2.0b12pre) Gecko/20110204 Firefox/4.0b12pre</li>
 <li>Mozilla/5.0 (Windows NT 10.0; Win64; x64; Xbox; Xbox One) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36 Edge/44.18363.8131</li>
 <li>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1)</li>
 <li>Mozilla/4.0 (compatible; MSIE 4.5; Windows 98;)</li>
 <li>curb</li>
 <li>bitdiscovery</li>
 <li>omgili/0.5 +http://omgili.com</li>
 <li>Mozilla/5.0 (compatible)</li>
 <li>Vizzit</li>
 <li>Mozilla/5.0 (Windows NT 5.1; rv:52.0) Gecko/20100101 Firefox/52.0</li>
 <li>Mozilla/5.0 (Android; Mobile; rv:13.0) Gecko/13.0 Firefox/13.0</li>
 <li>Java/17-ea</li>
 <li>AdobeUxTechC4-Async/3.0.12 (win32)</li>
 <li>ZaloPC-win32-24v473</li>
 <li>Mozilla/5.0/Firefox/42.0 - nbertaupete95(at)gmail.com</li>
 <li>Scoop.it</li>
 <li>Mozilla/5.0 (Windows NT 6.1; rv:27.0) Gecko/20100101 Firefox/27.0</li>
 <li>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</li>
 <li>ows NT 10.0; WOW64; rv: 50.0) Gecko/20100101 Firefox/50.0</li>
 <li>WebAPIClient</li>
 <li>Mozilla/5.0 Firefox/26.0</li>
 <li>Mozilla/5.0 (compatible; woorankreview/2.0; +https://www.woorank.com/)</li>
 </ul>
 </li>
 <li>For example, some are apparently using versions of Firefox that are over ten years old, and some are obviously trying to look like valid user agents, but making typos (<code>Mozilla / 5.0</code>)</li>
 <li>Tons of hosts making requests likt this:</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>GET /bitstream/handle/10568/109408/Milk%20testing%20lab%20protocol.pdf?sequence=1&amp;isAllowed=\x22&gt;&lt;script%20&gt;alert(String.fromCharCode(88,83,83))&lt;/script&gt; HTTP/1.1&#34; 400 5 &#34;-&#34; &#34;Mozilla/5.0 (Windows NT 10.0; WOW64; Rv:50.0) Gecko/20100101 Firefox/50.0
 </span></span></code></pre></div><ul>
 <li>I got a list of hosts making requests like that so I can purge their hits:</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># zcat /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.<span style="color:#f92672">[</span>123<span style="color:#f92672">]</span>*.gz | grep <span style="color:#e6db74">&#39;String.fromCharCode(&#39;</span> | awk <span style="color:#e6db74">&#39;{print $1}&#39;</span> | sort -u &gt; /tmp/ips.txt 
 </span></span></code></pre></div><ul>
 <li>I purged 4,718 hits from IPs</li>
 <li>I see some new Hetzner ranges that I hadn&rsquo;t blocked yet apparently?
 <ul>
 <li>I got a <a href="https://www.ipqualityscore.com/asn-details/AS24940/hetzner-online-gmbh">list of Hetzner&rsquo;s IPs from IP Quality Score</a> then added them to the existing ones in my Ansible playbooks:</li>
 </ul>
 </li>
 </ul>
 <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ awk <span style="color:#e6db74">&#39;{print $1}&#39;</span> /tmp/hetzner.txt | wc -l
 </span></span><span style="display:flex;"><span>36
 </span></span><span style="display:flex;"><span>$ sort -u /tmp/hetzner-combined.txt  | wc -l
 </span></span><span style="display:flex;"><span>49
 </span></span></code></pre></div><ul>
 <li>I will add this new list to nginx&rsquo;s <code>bot-networks.conf</code> so they get throttled on scraping XMLUI and get classified as bots in Solr statistics</li>
 <li>Then I purged hits from the following user agents:</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-spider-hits.sh -f /tmp/agents
 </span></span><span style="display:flex;"><span>Found 374 hits from curb in statistics
 </span></span><span style="display:flex;"><span>Found 350 hits from bitdiscovery in statistics
 </span></span><span style="display:flex;"><span>Found 564 hits from omgili in statistics
 </span></span><span style="display:flex;"><span>Found 390 hits from Vizzit in statistics
 </span></span><span style="display:flex;"><span>Found 9125 hits from AdobeUxTechC4-Async in statistics
 </span></span><span style="display:flex;"><span>Found 97 hits from ZaloPC-win32-24v473 in statistics
 </span></span><span style="display:flex;"><span>Found 518 hits from nbertaupete95 in statistics
 </span></span><span style="display:flex;"><span>Found 218 hits from Scoop.it in statistics
 </span></span><span style="display:flex;"><span>Found 584 hits from WebAPIClient in statistics
 </span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
 </span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of hits from bots: 12220
 </span></span></code></pre></div><ul>
 <li>Then I will add these user agents to the ILRI spider override in DSpace</li>
 </ul>
 <h2 id="2022-09-06">2022-09-06</h2>
 <ul>
 <li>I&rsquo;m testing dspace-statistics-api with our DSpace 7 test server
 <ul>
 <li>After setting up the env and the database the <code>python -m dspace_statistics_api.indexer</code> runs without issues</li>
 <li>While playing with Solr I tried to search for statistics from this month using <code>time:2022-09*</code> but I get this error: &ldquo;Can&rsquo;t run prefix queries on numeric fields&rdquo;</li>
 <li>I guess that the syntax in Solr changed since 4.10&hellip;</li>
 <li>This works, but is super annoying: <code>time:[2022-09-01T00:00:00Z TO 2022-09-30T23:59:59Z]</code></li>
 </ul>
 </li>
 </ul>
 <h2 id="2022-09-07">2022-09-07</h2>
 <ul>
 <li>I tested the controlled-vocabulary changes on DSpace 6 and they work fine
 <ul>
 <li>Last week I found that DSpace 7 is more strict with controlled vocabularies and requires IDs for all node values</li>
 <li>This is a pain because it means I have to re-do the IDs in each file every time I update them</li>
 <li>If I add <code>id=&quot;0000&quot;</code> to each, then I can use <a href="https://vim.fandom.com/wiki/Making_a_list_of_numbers#Substitute_with_ascending_numbers">this vim expression</a> <code>let i=0001 | g/0000/s//\=i/ | let i=i+1</code> to replace the numbers with increments starting from 1</li>
 </ul>
 </li>
 <li>Meeting with Marie Angelique, Abenet, Sarа, аnd Margarita to continue the discussion about Types from last week
 <ul>
 <li>We made progress with concrete actions and will continue next week</li>
 </ul>
 </li>
 </ul>
 <h2 id="2022-09-08">2022-09-08</h2>
 <ul>
 <li>I had a meeting with Nicky from UNEP to discuss issues they are having with their DSpace
 <ul>
 <li>I told her about the meeting of DSpace community people that we&rsquo;re planning at ILRI in the next few weeks</li>
 </ul>
 </li>
 </ul>
 <h2 id="2022-09-09">2022-09-09</h2>
 <ul>
 <li>Add some value mappings to AReS because I see a lot of incorrect regions and countries</li>
 <li>I also found some values that were blank in CGSpace so I deleted them:</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>dspace=# BEGIN;
 </span></span><span style="display:flex;"><span>BEGIN
 </span></span><span style="display:flex;"><span>dspace=# DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value=&#39;&#39;;
 </span></span><span style="display:flex;"><span>DELETE 70
 </span></span><span style="display:flex;"><span>dspace=# COMMIT;
 </span></span><span style="display:flex;"><span>COMMIT
 </span></span></code></pre></div><ul>
 <li>Start a full Discovery index on CGSpace to catch these changes in the Discovery</li>
 </ul>
 <h2 id="2022-09-11">2022-09-11</h2>
 <ul>
 <li>Today is Sunday and I see the load on the server is high
 <ul>
 <li>Google and a bunch of other bots have been blocked on XMLUI for the past two weeks so it&rsquo;s not from them!</li>
 <li>Looking at the top IPs this morning:</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># cat /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.1 | grep <span style="color:#e6db74">&#39;11/Sep/2022&#39;</span> | awk <span style="color:#e6db74">&#39;{print $1}&#39;</span> | sort | uniq -c | sort -h | tail -n <span style="color:#ae81ff">40</span>
 </span></span><span style="display:flex;"><span>...
 </span></span><span style="display:flex;"><span>    165 64.233.172.79
 </span></span><span style="display:flex;"><span>    166 87.250.224.34
 </span></span><span style="display:flex;"><span>    200 69.162.124.231
 </span></span><span style="display:flex;"><span>    202 216.244.66.198
 </span></span><span style="display:flex;"><span>    385 207.46.13.149
 </span></span><span style="display:flex;"><span>    398 207.46.13.147
 </span></span><span style="display:flex;"><span>    421 66.249.64.185
 </span></span><span style="display:flex;"><span>    422 157.55.39.81
 </span></span><span style="display:flex;"><span>    442 2a01:4f8:1c17:5550::1
 </span></span><span style="display:flex;"><span>    451 64.124.8.36
 </span></span><span style="display:flex;"><span>    578 137.184.159.211
 </span></span><span style="display:flex;"><span>    597 136.243.228.195
 </span></span><span style="display:flex;"><span>   1185 66.249.64.183
 </span></span><span style="display:flex;"><span>   1201 157.55.39.80
 </span></span><span style="display:flex;"><span>   3135 80.248.237.167
 </span></span><span style="display:flex;"><span>   4794 54.195.118.125
 </span></span><span style="display:flex;"><span>   5486 45.5.186.2
 </span></span><span style="display:flex;"><span>   6322 2a01:7e00::f03c:91ff:fe9a:3a37
 </span></span><span style="display:flex;"><span>   9556 66.249.64.181
 </span></span></code></pre></div><ul>
 <li>The top is still Google, but all the requests are HTTP 503 because I classified them as bots for XMLUI at least</li>
 <li>Then there&rsquo;s 80.248.237.167, which is using a normal user agent and scraping Discovery
 <ul>
 <li>That IP is on Internet Vikings aka Internetbolaget and we are already marking that subnet as &lsquo;bot&rsquo; for XMLUI so most of these requests are HTTP 503</li>
 </ul>
 </li>
 <li>On another note, I&rsquo;m curious to explore enabling caching of certain REST API responses
 <ul>
 <li>For example, where the use is for harvesting rather than actual clients getting bitstreams or thumbnails, it seems there might be a benefit to speeding these up for subsequent requestors:</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># awk <span style="color:#e6db74">&#39;{print $7}&#39;</span> /var/log/nginx/rest.log | grep -v retrieve | sort | uniq -c | sort -h | tail -n <span style="color:#ae81ff">10</span>
 </span></span><span style="display:flex;"><span>      4 /rest/items/3f692ddd-7856-4bf0-a587-99fb3df0688a/bitstreams
 </span></span><span style="display:flex;"><span>      4 /rest/items/3f692ddd-7856-4bf0-a587-99fb3df0688a/metadata
 </span></span><span style="display:flex;"><span>      4 /rest/items/b014e36f-b496-43d8-9148-cc9db8a6efac/bitstreams
 </span></span><span style="display:flex;"><span>      4 /rest/items/b014e36f-b496-43d8-9148-cc9db8a6efac/metadata
 </span></span><span style="display:flex;"><span>      5 /rest/handle/10568/110310?expand=all
 </span></span><span style="display:flex;"><span>      5 /rest/handle/10568/89980?expand=all
 </span></span><span style="display:flex;"><span>      5 /rest/handle/10568/97614?expand=all
 </span></span><span style="display:flex;"><span>      6 /rest/handle/10568/107086?expand=all
 </span></span><span style="display:flex;"><span>      6 /rest/handle/10568/108503?expand=all
 </span></span><span style="display:flex;"><span>      6 /rest/handle/10568/98424?expand=all
 </span></span></code></pre></div><ul>
 <li>I specifically have to not cache things like requests for bitstreams because those are from actual users and we need to keep the real requests so we get the statistics hit
 <ul>
 <li>Will be interesting to check the results above as the day goes on (now 10AM)</li>
 <li>To estimate the potential savings from caching I will check how many non-bitstream requests are made versus how many are made more than once (updated the next morning using yesterday&rsquo;s log):</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># awk <span style="color:#e6db74">&#39;{print $7}&#39;</span> /var/log/nginx/rest.log.1 | grep -v retrieve | sort -u | wc -l
 </span></span><span style="display:flex;"><span>33733
 </span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">&#39;{print $7}&#39;</span> /var/log/nginx/rest.log.1 | grep -v retrieve | sort | uniq -c | awk <span style="color:#e6db74">&#39;$1 &gt; 1&#39;</span> | wc -l
 </span></span><span style="display:flex;"><span>5637
 </span></span></code></pre></div><ul>
 <li>In the afternoon I started a harvest on AReS (which should affect the numbers above also)</li>
 <li>I enabled an nginx proxy cache on DSpace Test for this location regex: <code>location ~ /rest/(handle|items|collections|communities)/.+</code></li>
 </ul>
 <h2 id="2022-09-12">2022-09-12</h2>
 <ul>
 <li>I am testing harvesting DSpace Test via AReS with the nginx proxy cache enabled
 <ul>
 <li>I had to tune the regular expression in nginx a bit because the REST requests OpenRXV uses weren&rsquo;t matching</li>
 <li>Now I&rsquo;m trying this one: <code>/rest/(handle|items|collections|communities)/?</code></li>
 <li>Testing in <a href="https://regex101.com/r/vPz11y/1">regex101.com</a> with this test string:</li>
 </ul>
 </li>
 </ul>
 <pre tabindex="0"><code>/rest/handle/10568/27611
 /rest/items?expand=metadata,parentCommunityList,parentCollectionList,bitstreams&amp;limit=10&amp;offset=36270
 /rest/handle/10568/110310?expand=all
 /rest/rest/bitstreams/28926633-c7c2-49c2-afa8-6d81cadc2316/retrieve
 /rest/bitstreams/15412/retrieve
 /rest/items/083dbb0d-11e2-4dfe-902b-eb48e4640d04/metadata
 /rest/items/083dbb0d-11e2-4dfe-902b-eb48e4640d04/bitstreams
 /rest/collections/edea23c0-0ebd-4525-90b0-0b401f997704/items
 /rest/items/14507941-aff2-4d57-90bd-03a0733ad859/metadata
 /rest/communities/b38ea726-475f-4247-a961-0d0b76e67f85/collections
 /rest/collections/e994c450-6ff7-41c6-98df-51e5c424049e/items?limit=10000
 </code></pre><ul>
 <li>I estimate that it will take about 1GB of cache to harvest 100,000 items from CGSpace with OpenRXV (10,000 pages)</li>
 <li>Basically all but 4 and 5 (bitstreams) should match</li>
 <li>Upload 682 OICRs from MARLO to CGSpace
 <ul>
 <li>We had tested these on DSpace Test last month along with the MELIAs, Policies, and Innovations, but we decided to upload the OICRs first so that other things can link against them as related items</li>
 </ul>
 </li>
 </ul>
 <h2 id="2022-09-14">2022-09-14</h2>
 <ul>
 <li>Meeting with Peter, Abenet, Indira, and Michael about CGSpace rollout plan for the Initiatives</li>
 </ul>
 <h2 id="2022-09-16">2022-09-16</h2>
 <ul>
 <li>Meeting with Marie-Angeqlique, Abenet, Margarita, and Sara about types for CG Core
 <ul>
 <li>We are about halfway through the list of types now, with concrete actions for CG Core and CGSpace</li>
 <li>We will meet next in two weeks to hopefully finalize the list, then we can move on to definitions</li>
 </ul>
 </li>
 </ul>
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 <li><a href="/cgspace-notes/2022-09/">September, 2022</a></li>
 <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>
 <li><a href="/cgspace-notes/2022-05/">May, 2022</a></li>
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    <ol class="list-unstyled">
      <li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
      <li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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