2022-06-06 08:45:43 +02:00
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Look at the Solr statistics on CGSpace
I see 167,000 hits from a bunch of Microsoft IPs with reverse DNS “ msnbot-” using the Solr query dns:*msnbot* AND dns:*.msn.com
I purged these first so I could see the other “ real” IPs in the Solr facets
I see 47,500 hits from 80.248.237.167 on a data center ISP in Sweden, using a normal user agent
I see 13,000 hits from 163.237.216.11 on a data center ISP in Australia, using a normal user agent
I see 7,300 hits from 208.185.238.57 from Britanica, using a normal user agent
There seem to be many more of these:
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2023-05-02 09:39:34 +02:00
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2022-06-06 08:45:43 +02:00
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< meta name = "twitter:title" content = "June, 2022" / >
< meta name = "twitter:description" content = "2022-06-06
Look at the Solr statistics on CGSpace
I see 167,000 hits from a bunch of Microsoft IPs with reverse DNS “ msnbot-” using the Solr query dns:*msnbot* AND dns:*.msn.com
I purged these first so I could see the other “ real” IPs in the Solr facets
I see 47,500 hits from 80.248.237.167 on a data center ISP in Sweden, using a normal user agent
I see 13,000 hits from 163.237.216.11 on a data center ISP in Australia, using a normal user agent
I see 7,300 hits from 208.185.238.57 from Britanica, using a normal user agent
There seem to be many more of these:
"/>
2023-03-21 14:35:41 +01:00
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2022-06-06 08:45:43 +02:00
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2022-06-06 08:45:43 +02:00
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2022-06-06 08:45:43 +02:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2022-06/" > June, 2022< / a > < / h2 >
< p class = "blog-post-meta" >
< time datetime = "2022-06-06T09:01:36+03:00" > Mon Jun 06, 2022< / time >
in
2022-06-23 07:40:53 +02:00
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
2022-06-06 08:45:43 +02:00
< / p >
< / header >
< h2 id = "2022-06-06" > 2022-06-06< / h2 >
< ul >
< li > Look at the Solr statistics on CGSpace
< ul >
< li > I see 167,000 hits from a bunch of Microsoft IPs with reverse DNS “ msnbot-” using the Solr query < code > dns:*msnbot* AND dns:*.msn.com< / code > < / li >
< li > I purged these first so I could see the other “ real” IPs in the Solr facets< / li >
< / ul >
< / li >
< li > I see 47,500 hits from 80.248.237.167 on a data center ISP in Sweden, using a normal user agent< / li >
< li > I see 13,000 hits from 163.237.216.11 on a data center ISP in Australia, using a normal user agent< / li >
< li > I see 7,300 hits from 208.185.238.57 from Britanica, using a normal user agent
< ul >
< li > There seem to be many more of these:< / 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 > # zcat --force /var/log/nginx/access.log* | grep 208.185.238. | awk < span style = "color:#e6db74" > ' {print $1}' < / span > | sort | uniq -c | sort -h
< / span > < / span > < span style = "display:flex;" > < span > 2 208.185.238.1
< / span > < / span > < span style = "display:flex;" > < span > 166 208.185.238.54
< / span > < / span > < span style = "display:flex;" > < span > 1293 208.185.238.51
< / span > < / span > < span style = "display:flex;" > < span > 2587 208.185.238.59
< / span > < / span > < span style = "display:flex;" > < span > 4692 208.185.238.56
< / span > < / span > < span style = "display:flex;" > < span > 5480 208.185.238.53
< / span > < / span > < span style = "display:flex;" > < span > 6277 208.185.238.52
< / span > < / span > < span style = "display:flex;" > < span > 6400 208.185.238.58
< / span > < / span > < span style = "display:flex;" > < span > 8261 208.185.238.55
< / span > < / span > < span style = "display:flex;" > < span > 17549 208.185.238.57
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > I see 3,000 hits from 178.208.75.33 by a Russian-owned IP in the Netherlands that is making a GET to / every one minute, using a normal user agent< / li >
< li > I see 3,000 hits from 134.122.124.196 on Digital Ocean to the REST API with a normal user agent< / li >
< li > I purged all these hits from IPs for a total of about 265,000< / li >
< li > Then I faceted by user agent and found
< ul >
< li > 1,000 hits by < code > insomnia/2022.2.1< / code > , which I also saw last month and submitted to COUNTER-Robots< / li >
< li > 265 hits by < code > omgili/0.5 +http://omgili.com< / code > < / li >
< li > 150 hits by < code > Vizzit< / code > < / li >
< li > 132 hits by < code > MetaInspector/5.7.0 (+https://github.com/jaimeiniesta/metainspector)< / code > < / li >
< li > 73 hits by < code > Scoop.it< / code > < / li >
< li > 62 hits by < code > bitdiscovery< / code > < / li >
< li > 59 hits by < code > Asana/1.4.0 WebsiteMetadataRetriever< / code > < / li >
< li > 32 hits by < code > Sprout Social (Link Attachment)< / code > < / li >
< li > 29 hits by < code > CyotekWebCopy/1.9 CyotekHTTP/6.2< / code > < / li >
< li > 20 hits by < code > Hootsuite-Authoring/1.0< / code > < / li >
< / ul >
< / li >
< li > I purged about 4,100 hits from these user agents< / li >
2022-06-06 15:54:08 +02:00
< li > Run all system updates on AReS server (linode20) and reboot< / li >
< li > I want to try to update some of the build dependencies of OpenRXV since Node.js 12 is no longer supported< / li >
< li > Upgrade linode20 to Ubuntu 22.04 and start an AReS harvest< / li >
2022-06-08 14:36:09 +02:00
< li > I merged the < a href = "https://github.com/DSpace/DSpace/pull/8292" > Mirage 2 build fix< / a > to < code > dspace-6_x< / code > for DSpace 6.4< / li >
< / ul >
< h2 id = "2022-06-07" > 2022-06-07< / h2 >
< ul >
< li > I tested Node.js 14 one more time with vanilla DSpace 6.4-SNAPSHOT and with the CGSpace source and it worked well
< ul >
< li > I made < a href = "https://github.com/DSpace/DSpace/pull/8331" > a pull request< / a > to DSpace to use Node.js 14 for Mirage 2< / li >
< li > I even tested Node.js 16 and it works, but that is enough for now… < / li >
< / ul >
< / li >
< / ul >
< h2 id = "2022-06-08" > 2022-06-08< / h2 >
< ul >
< li > Work on AReS a bit since I wasn’ t able to harvest after doing the updates on the server and in the containers a few days ago
< ul >
< li > I don’ t know what the problem was really, but on the server I had to enable IPv4 forwarding so the frontend container would build< / li >
< li > Once I downed and upped AReS with docker-compose I was able to start a new harvest< / li >
< li > I also did some tests to enable ES2020 target in the backend because we’ re on Node.js 14 there now< / li >
< / ul >
< / li >
2022-06-06 08:45:43 +02:00
< / ul >
2022-06-14 07:45:07 +02:00
< h2 id = "2022-06-13" > 2022-06-13< / h2 >
< ul >
< li > Create a user for Mohammed Salem to test MEL submission on 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 > $ dspace user -a -m mel-submit@cgiar.org -g MEL -s Submit -p < span style = "color:#e6db74" > ' owwwwwwww' < / span >
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > According to my notes from < a href = "/cgspace-notes/2020-10/" > 2020-10< / a > the account must be in the admin group in order to submit via the REST API< / li >
< / ul >
2022-06-16 15:25:51 +02:00
< h2 id = "2022-06-14" > 2022-06-14< / h2 >
< ul >
< li > Start a harvest on AReS< / li >
< / ul >
< h2 id = "2022-06-16" > 2022-06-16< / h2 >
< ul >
< li > Francesca asked us to add the CC-BY-3.0-IGO license to the submission form on CGSpace
< ul >
< li > I remember I < a href = "https://github.com/spdx/license-list-XML/issues/767" > had requested SPDX to add CC-BY-NC-ND-3.0-IGO< / a > in 2019-02, and they finally < a href = "https://github.com/spdx/license-list-XML/pull/1068" > merged it< / a > in 2020-07, but I never added it to CGSpace< / li >
< li > I will add the full suite of CC 3.0 IGO licenses to CGSpace and then make a request to SPDX for the others:
- CC-BY-3.0-IGO
- CC-BY-SA-3.0-IGO
- CC-BY-ND-3.0-IGO
- CC-BY-NC-3.0-IGO
- CC-BY-NC-SA-3.0-IGO
- CC-BY-NC-ND-3.0-IGO< / li >
< / ul >
< / li >
< li > I filed < a href = "https://github.com/spdx/license-list-XML/issues/1525" > an issue asking for SPDX to add CC-BY-3.0-IGO< / a > < / li >
< li > Meeting with Moayad from CodeObia to discuss OpenRXV
< ul >
< li > He added the ability to use multiple indexes / dashboards, and to be able to embed them in iframes< / li >
< / ul >
< / li >
< li > Add < code > cg.contributor.initiative< / code > with a controlled vocabulary based on CLARISA’ s list to the CGSpace submission form< / li >
2022-06-16 18:51:59 +02:00
< li > Switch to the < code > linux-virtual-hwe-20.04< / code > kernel on CGSpace (linode18), run all system updates, and reboot< / li >
2022-06-16 15:25:51 +02:00
< / ul >
2022-06-17 15:46:56 +02:00
< h2 id = "2022-06-17" > 2022-06-17< / h2 >
< ul >
< li > I noticed a few ORCID identifiers missing for some scientists so I added them to the controlled vocabulary and then tagged them on CGSpace:< / 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 2022-06-17-add-orcids.csv
< / span > < / span > < span style = "display:flex;" > < span > dc.contributor.author,cg.creator.identifier
< / span > < / span > < span style = "display:flex;" > < span > " Tijjani, A." ," Abdulfatai Tijjani: 0000-0002-0793-9059"
< / span > < / span > < span style = "display:flex;" > < span > " Tijjani, Abdulfatai" ," Abdulfatai Tijjani: 0000-0002-0793-9059"
< / span > < / span > < span style = "display:flex;" > < span > " Mrode, Raphael A." ," Raphael Mrode: 0000-0003-1964-5653"
< / span > < / span > < span style = "display:flex;" > < span > " Okeyo Mwai, Ally" ," Ally Okeyo Mwai: 0000-0003-2379-7801"
< / span > < / span > < span style = "display:flex;" > < span > " Ojango, Julie M.K." ," Ojango J.M.K.: 0000-0003-0224-5370"
< / span > < / span > < span style = "display:flex;" > < span > " Prendergast, J.G.D." ," James Prendergast: 0000-0001-8916-018X"
< / span > < / span > < span style = "display:flex;" > < span > " Ekine-Dzivenu, Chinyere" ," Chinyere Ekine-Dzivenu: 0000-0002-8526-435X"
< / span > < / span > < span style = "display:flex;" > < span > " Ekine, C." ," Chinyere Ekine-Dzivenu: 0000-0002-8526-435X"
< / span > < / span > < span style = "display:flex;" > < span > " Ekine-Dzivenu, C.C" ," Chinyere Ekine-Dzivenu: 0000-0002-8526-435X"
< / span > < / span > < span style = "display:flex;" > < span > " Shilomboleni, Helena" ," Helena Shilomboleni: 0000-0002-9875-6484"
< / span > < / span > < span style = "display:flex;" > < span > $ ./ilri/add-orcid-identifiers-csv.py -i /tmp/2022-06-17-add-orcids.csv -db dspace -u dspace -p < span style = "color:#e6db74" > ' fuuu' < / span > | tee /tmp/orcids.log
< / span > < / span > < span style = "display:flex;" > < span > $ grep -c < span style = "color:#e6db74" > ' Adding ORCID' < / span > /tmp/orcids2.log
< / span > < / span > < span style = "display:flex;" > < span > 304
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > Also make some changes to the Discovery facets and item view
< ul >
< li > I reduced the number of items to show for CRP facets from 20 to 5< / li >
< li > I added a facet for the Initiatives< / li >
< li > I re-organized a few parts of the item view to add Action Areas and the list of author affiliations< / li >
< / ul >
< / li >
< / ul >
2022-06-18 19:39:37 +02:00
< h2 id = "2022-06-18" > 2022-06-18< / h2 >
< ul >
< li > I deployed the changes on CGSpace and started a full Discovery index for the new Initiatives facet< / li >
< li > Run < code > dspace cleanup -v< / code > on CGSpace< / li >
< / ul >
2022-06-21 15:59:04 +02:00
< h2 id = "2022-06-20" > 2022-06-20< / h2 >
< ul >
< li > Add missing ORCID identifier for ILRI staff to CGSpace and tag their items< / li >
< / ul >
< h2 id = "2022-06-21" > 2022-06-21< / h2 >
< ul >
< li > Work on OpenRXV backend dependencies
< ul >
< li > Update Elasticsearch and TypeScript and eslint< / li >
< / ul >
< / li >
< li > Sit in on webinar about contributing terms to AGROVOC
< ul >
< li > I agreed that I would send Sara Jani from ICARDA a list of new terms we have that don’ t match AGROVOC by end of June< / li >
< li > I need to indicate which center is using them so we can have an appropriate expert review the terms< / li >
< / ul >
< / li >
< / ul >
2022-06-23 07:40:53 +02:00
< h2 id = "2022-06-22" > 2022-06-22< / h2 >
< ul >
< li > I re-deployed AReS with the latest OpenRXV changes then started a fresh harvest< / li >
< li > Meeting with Salem to discuss metadata between CGSpace and MEL
< ul >
< li > We started working through his spreadsheet and then the Internet dropped< / li >
< / ul >
< / li >
< / ul >
2022-06-24 13:49:37 +02:00
< h2 id = "2022-06-23" > 2022-06-23< / h2 >
< ul >
< li > Start looking at country names between MEL, CGSpace, and standards like UN M.49 and GeoNames
< ul >
< li > I used < code > xmllint< / code > to extract the countries from CGSpace’ s input forms:< / 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 > $ xmllint --xpath < span style = "color:#e6db74" > ' //value-pairs[@value-pairs-name=" countrylist" ]/pair/stored-value/node()' < / span > dspace/config/input-forms.xml > /tmp/cgspace-countries.txt
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > Then I wrote a Python script (< code > countries-to-csv.py< / code > ) to read them and save their names alongside the ISO 3166-1 Alpha2 code< / li >
< li > Then I joined them with the other lists:< / 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 --outer -c alpha2 ~/Downloads/clarisa-countries.csv ~/Downloads/UNSD< span style = "color:#ae81ff" > \ < / span > —< span style = "color:#ae81ff" > \ < / span > Methodology.csv ~/Downloads/geonames-countries.csv /tmp/cgspace-countries.csv /tmp/mel-countries.csv> /tmp/countries.csv
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > This mostly worked fine, and is much easier than writing another Python script with Pandas… < / li >
< / ul >
< h2 id = "2022-06-24" > 2022-06-24< / h2 >
< ul >
< li > Spent some more time working on my < code > countries-to-csv.py< / code > script to fix some logic errors< / li >
< li > Then re-export the UN M.49 countries to a clean list because the one I did yesterday somehow has errors:< / 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 -d ' ;' -c ' ISO-alpha2 Code,Country or Area' ~/Downloads/UNSD\ —\ Methodology.csv | sed -e ' 1s/ISO-alpha2 Code/alpha2/' -e ' 1s/Country or Area/UN M.49 Name/' > ~/Downloads/un-countries.csv
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > Check the number of lines in each file:< / li >
< / ul >
< pre tabindex = "0" > < code > $ wc -l clarisa-countries.csv un-countries.csv cgspace-countries.csv mel-countries.csv
250 clarisa-countries.csv
250 un-countries.csv
198 cgspace-countries.csv
258 mel-countries.csv
< / code > < / pre > < ul >
< li > I am seeing strange results with csvjoin’ s < code > --outer< / code > join that I need to keep unmatched terms from both left and right files…
< ul >
< li > Using < code > xsv join --full< / code > is giving me better results:< / li >
< / ul >
< / li >
< / ul >
< pre tabindex = "0" > < code > $ xsv join --full alpha2 ~/Downloads/clarisa-countries.csv alpha2 ~/Downloads/un-countries.csv | xsv select ' !alpha2[1]' > /tmp/clarisa-un-xsv-full.csv
< / code > < / pre > < ul >
< li > Then adding the CGSpace and MEL countries:< / 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 --full alpha2 /tmp/clarisa-un-xsv-full.csv alpha2 /tmp/cgspace-countries.csv | xsv < span style = "color:#66d9ef" > select< / span > < span style = "color:#e6db74" > ' !alpha2[1]' < / span > > /tmp/clarisa-un-cgspace-xsv-full.csv
< / span > < / span > < span style = "display:flex;" > < span > $ xsv join --full alpha2 /tmp/clarisa-un-cgspace-xsv-full.csv alpha2 /tmp/mel-countries.csv | xsv < span style = "color:#66d9ef" > select< / span > < span style = "color:#e6db74" > ' !alpha2[1]' < / span > > /tmp/clarisa-un-cgspace-mel-xsv-full.csv
2022-06-26 17:11:33 +02:00
< / span > < / span > < / code > < / pre > < / div > < h2 id = "2022-06-26" > 2022-06-26< / h2 >
< ul >
< li > Start a harvest on AReS< / li >
< / ul >
2022-06-30 08:41:54 +02:00
< h2 id = "2022-06-28" > 2022-06-28< / h2 >
< ul >
2023-04-27 22:10:13 +02:00
< li > Start working on the CGSpace subject export for FAO / AGROVOC< / li >
2022-06-30 08:41:54 +02:00
< li > First I exported a list of all metadata in our < code > dcterms.subject< / code > and other center-specific subject fields with their counts:< / 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 > localhost/dspacetest= ☘ \COPY (SELECT DISTINCT text_value AS " subject" , count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (187, 120, 210, 122, 215, 127, 208, 124, 128, 123, 125, 135, 203, 236, 238, 119) GROUP BY " subject" ORDER BY count DESC) to /tmp/2022-06-28-cgspace-subjects.csv WITH CSV HEADER;
< / span > < / span > < span style = "display:flex;" > < span > COPY 27010
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > Then I extracted the subjects and looked them up against AGROVOC:< / 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 subject /tmp/2022-06-28-cgspace-subjects.csv | sed < span style = "color:#e6db74" > ' 1d' < / span > > /tmp/2022-06-28-cgspace-subjects.txt
< / span > < / span > < span style = "display:flex;" > < span > $ ./ilri/agrovoc-lookup.py -i /tmp/2022-06-28-cgspace-subjects.txt -o /tmp/2022-06-28-cgspace-subjects-results.csv
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > I keep getting timeouts after every five or ten requests, so this will not be feasible for 27,000 subjects!< / li >
< li > I think I will have to write some custom script to use the AGROVOC RDF file
< ul >
< li > Using rdflib to open the 1.2GB < code > agrovoc_lod.rdf< / code > file takes several minutes and doesn’ t seem very efficient< / li >
< / ul >
< / li >
2023-04-27 22:10:13 +02:00
< li > I tried using < a href = "https://github.com/ozekik/lightrdf" > lightrdf< / a > and it’ s much quicker, but the documentation is limited and I’ m not sure how to search yet
2022-06-30 08:41:54 +02:00
< ul >
< li > I had to try in different Python versions because 3.10.x is apparently too new< / li >
< / ul >
< / li >
< li > For future reference I was able to search with lightrdf:< / li >
< / ul >
2022-08-03 20:01:39 +02:00
< 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:#f92672" > import< / span > lightrdf
< / span > < / span > < span style = "display:flex;" > < span > parser < span style = "color:#f92672" > =< / span > lightrdf< span style = "color:#f92672" > .< / span > Parser()
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#75715e" > # prints millions of lines< / span >
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#66d9ef" > for< / span > triple < span style = "color:#f92672" > in< / span > parser< span style = "color:#f92672" > .< / span > parse(< span style = "color:#e6db74" > " ./agrovoc_lod.rdf" < / span > , base_iri< span style = "color:#f92672" > =< / span > < span style = "color:#66d9ef" > None< / span > ):
2022-06-30 08:41:54 +02:00
< / span > < / span > < span style = "display:flex;" > < span > print(triple)
2022-08-03 20:01:39 +02:00
< / span > < / span > < span style = "display:flex;" > < span > agrovoc < span style = "color:#f92672" > =< / span > lightrdf< span style = "color:#f92672" > .< / span > RDFDocument(< span style = "color:#e6db74" > ' agrovoc_lod.rdf' < / span > );
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#75715e" > # all results for prefix http://aims.fao.org/aos/agrovoc/c_5< / span >
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#66d9ef" > for< / span > triple < span style = "color:#f92672" > in< / span > agrovoc< span style = "color:#f92672" > .< / span > search_triples(< span style = "color:#e6db74" > ' http://aims.fao.org/aos/agrovoc/c_5' < / span > , < span style = "color:#66d9ef" > None< / span > , < span style = "color:#66d9ef" > None< / span > ):
2022-06-30 08:41:54 +02:00
< / span > < / span > < span style = "display:flex;" > < span > print(triple)
2022-08-03 20:01:39 +02:00
< / span > < / span > < span style = "display:flex;" > < span > (< span style = "color:#e6db74" > ' http://aims.fao.org/aos/agrovoc/c_5' < / span > , < span style = "color:#e6db74" > ' http://www.w3.org/2004/02/skos/core#altLabel' < / span > , < span style = "color:#e6db74" > ' " Abalone" @de' < / span > )
< / span > < / span > < span style = "display:flex;" > < span > (< span style = "color:#e6db74" > ' http://aims.fao.org/aos/agrovoc/c_5' < / span > , < span style = "color:#e6db74" > ' http://www.w3.org/2004/02/skos/core#prefLabel' < / span > , < span style = "color:#e6db74" > ' " abalones" @en' < / span > )
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#75715e" > # all stuff for abalones in English< / span >
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#66d9ef" > for< / span > triple < span style = "color:#f92672" > in< / span > agrovoc< span style = "color:#f92672" > .< / span > search_triples(< span style = "color:#66d9ef" > None< / span > , < span style = "color:#66d9ef" > None< / span > , < span style = "color:#e6db74" > ' " abalones" @en' < / span > ):
2022-06-30 08:41:54 +02:00
< / span > < / span > < span style = "display:flex;" > < span > print(triple)
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > I ran the < code > agrovoc-lookup.py< / code > from a Linode server and it completed without issues… hmmm< / li >
< / ul >
< h2 id = "2022-06-29" > 2022-06-29< / h2 >
< ul >
< li > Continue working on the list of non-AGROVOC subject to report to FAO
< ul >
2022-06-30 15:48:03 +02:00
< li > I got a one liner to get the list of non-AGROVOC subjects and join them with their counts (updated to use regex in csvgrep):< / li >
2022-06-30 08:41:54 +02:00
< / ul >
< / li >
< / ul >
2022-06-30 15:48:03 +02:00
< 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 > $ csvgrep -c < span style = "color:#e6db74" > ' number of matches' < / span > -r < span style = "color:#e6db74" > ' ^0$' < / span > /tmp/2022-06-28-cgspace-subjects-results.csv < span style = "color:#ae81ff" > \
2022-06-30 08:41:54 +02:00
< / span > < / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#ae81ff" > < / span > | csvcut -c subject \
< / span > < / span > < span style = "display:flex;" > < span > | csvjoin -c subject /tmp/2022-06-28-cgspace-subjects.csv - \
< / span > < / span > < span style = "display:flex;" > < span > > /tmp/2022-06-28-cgspace-non-agrovoc.csv
2022-06-30 15:48:03 +02:00
< / span > < / span > < / code > < / pre > < / div > < h2 id = "2022-06-30" > 2022-06-30< / h2 >
< ul >
< li > Check some AfricaRice records for potential duplicates on CGSpace for Abenet:< / 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/Africarice_2ndBatch_ay.csv | sed < span style = "color:#e6db74" > ' 1s/line_number/id/' < / span > > /tmp/africarice.csv
< / span > < / span > < span style = "display:flex;" > < span > $ csv-metadata-quality -i /tmp/africarice.csv -o /tmp/africarice-cleaned.csv -u
< / span > < / span > < span style = "display:flex;" > < span > $ ./ilri/check-duplicates.py -i /tmp/africarice-cleaned.csv -u dspacetest -db dspacetest -p < span style = "color:#e6db74" > ' dom@in34sniper' < / span > -o /tmp/africarice-duplicates.csv
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > Looking at the non-AGROVOC subjects again, I see some in our list that are duplicated in uppercase and lowercase, so I will run it again with all lowercase:< / 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 > localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(lower(text_value)) AS " subject" , count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (187, 120, 210, 122, 215, 127, 208, 124, 128, 123, 125, 135, 203, 236, 238, 119) GROUP BY " subject" ORDER BY count DESC) to /tmp/2022-06-30-cgspace-subjects.csv WITH CSV HEADER;
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > Also, I see there might be something wrong with my csvjoin because nigeria shows up in the final list as having not matched…
< ul >
< li > Ah, I was using < code > csvgrep -m 0< / code > to find rows that didn’ t match, but that also matched items that had 10, 100, 50, etc… < / li >
< li > We need to use a regex:< / 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 > $ csvgrep -c < span style = "color:#e6db74" > ' number of matches' < / span > -r < span style = "color:#e6db74" > ' ^0$' < / span > /tmp/2022-06-30-cgspace-subjects-results.csv < span style = "color:#ae81ff" > \
< / span > < / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#ae81ff" > < / span > | csvcut -c subject \
< / span > < / span > < span style = "display:flex;" > < span > | csvjoin -c subject /tmp/2022-06-30-cgspace-subjects.csv - \
< / span > < / span > < span style = "display:flex;" > < span > > /tmp/2022-06-30-cgspace-non-agrovoc.csv
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > Then I took all the terms with fifty or more occurences and put them on a Google Sheet
< ul >
< li > There I started removing any term that was a variation of an existing AGROVOC term (like cowpea/cowpeas, policy/policies) or a compound concept< / li >
< / ul >
< / li >
2022-07-04 08:25:14 +02:00
< li > pnbecker on DSpace Slack mentioned that they made a JSPUI deduplication step that is open source: < a href = "https://github.com/the-library-code/deduplication" > https://github.com/the-library-code/deduplication< / a >
< ul >
< li > It uses Levenshtein distance via PostgreSQL’ s fuzzystrmatch extension< / li >
< / ul >
< / li >
2022-06-30 15:48:03 +02:00
< / ul >
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2022-06-06 08:45:43 +02:00
< / article >
< / div > <!-- /.blog - main -->
< aside class = "col-sm-3 ml-auto blog-sidebar" >
< section class = "sidebar-module" >
< h4 > Recent Posts< / h4 >
< ol class = "list-unstyled" >
2023-04-02 08:16:25 +02:00
< li > < a href = "/cgspace-notes/2023-04/" > April, 2023< / a > < / li >
2023-03-01 06:30:25 +01:00
< li > < a href = "/cgspace-notes/2023-03/" > March, 2023< / a > < / li >
2023-02-09 06:50:54 +01:00
< li > < a href = "/cgspace-notes/2023-02/" > February, 2023< / a > < / li >
2023-01-01 09:12:13 +01:00
< li > < a href = "/cgspace-notes/2023-01/" > January, 2023< / a > < / li >
2022-12-03 08:46:29 +01:00
< li > < a href = "/cgspace-notes/2022-12/" > December, 2022< / a > < / li >
2022-06-06 08:45:43 +02:00
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< / section >
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< h4 > Links< / h4 >
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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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