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Add notes for 2022-03-04
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@ -46,7 +46,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did
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The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes
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I ran all system updates on DSpace Test and rebooted it
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"/>
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<meta name="generator" content="Hugo 0.92.2" />
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<meta name="generator" content="Hugo 0.93.1" />
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@ -179,13 +179,13 @@ I ran all system updates on DSpace Test and rebooted it
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<li>I did some quick sanity checks and small cleanups in Open Refine, checking for spaces, weird accents, and encoding errors</li>
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<li>Finally I did a test run with the <a href="https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897"><code>fix-metadata-value.py</code></a> script:</li>
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</ul>
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i 2018-08-15-Correct-1083-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t correct -m 211
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$ ./delete-metadata-values.py -i 2018-08-15-Remove-11-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i 2018-08-15-Correct-1083-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t correct -m 211
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$ ./delete-metadata-values.py -i 2018-08-15-Remove-11-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211
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</code></pre><h2 id="2018-08-16">2018-08-16</h2>
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<ul>
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<li>Generate a list of the top 1,500 authors on CGSpace for Sisay so he can create the controlled vocabulary:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc limit 1500) to /tmp/2018-08-16-top-1500-authors.csv with csv;
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<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc limit 1500) to /tmp/2018-08-16-top-1500-authors.csv with csv;
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</code></pre><ul>
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<li>Start working on adding the ORCID metadata to a handful of CIAT authors as requested by Elizabeth earlier this month</li>
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<li>I might need to overhaul the <a href="https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050">add-orcid-identifiers-csv.py</a> script to be a little more robust about author order and ORCID metadata that might have been altered manually by editors after submission, as this script was written without that consideration</li>
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@ -198,14 +198,14 @@ $ ./delete-metadata-values.py -i 2018-08-15-Remove-11-Affiliations.csv -db dspac
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<pre tabindex="0"><code>$ sudo docker run --name dspacedb -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
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$ createuser -h localhost -U postgres --pwprompt dspacetest
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$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
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$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest ~/Downloads/cgspace_2018-08-16.backup
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
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$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
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</code></pre><h2 id="2018-08-19">2018-08-19</h2>
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<ul>
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<li>Keep working on the CIAT ORCID identifiers from Elizabeth</li>
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<li>In the spreadsheet she sent me there are some names with other versions in the database, so when it is obviously the same one (ie “Schultze-Kraft, Rainer” and “Schultze-Kraft, R.") I will just tag them with ORCID identifiers too</li>
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<li>In the spreadsheet she sent me there are some names with other versions in the database, so when it is obviously the same one (ie “Schultze-Kraft, Rainer” and “Schultze-Kraft, R.”) I will just tag them with ORCID identifiers too</li>
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<li>This is less obvious and more error prone with names like “Peters” where there are many more authors</li>
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<li>I see some errors in the variations of names as well, for example:</li>
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</ul>
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@ -221,37 +221,37 @@ Verchot, Louis V.
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<li>In the end, I’ll run the following CSV with my <a href="https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050">add-orcid-identifiers-csv.py</a> script:</li>
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</ul>
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<pre tabindex="0"><code>dc.contributor.author,cg.creator.id
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"Campbell, Bruce",Bruce M Campbell: 0000-0002-0123-4859
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"Campbell, Bruce M.",Bruce M Campbell: 0000-0002-0123-4859
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"Campbell, B.M",Bruce M Campbell: 0000-0002-0123-4859
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"Peters, Michael",Michael Peters: 0000-0003-4237-3916
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"Peters, M.",Michael Peters: 0000-0003-4237-3916
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"Peters, M.K.",Michael Peters: 0000-0003-4237-3916
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"Tamene, Lulseged",Lulseged Tamene: 0000-0002-3806-8890
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"Desta, Lulseged Tamene",Lulseged Tamene: 0000-0002-3806-8890
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"Läderach, Peter",Peter Läderach: 0000-0001-8708-6318
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"Lundy, Mark",Mark Lundy: 0000-0002-5241-3777
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"Schultze-Kraft, Rainer",Rainer Schultze-Kraft: 0000-0002-4563-0044
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"Schultze-Kraft, R.",Rainer Schultze-Kraft: 0000-0002-4563-0044
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"Verchot, Louis",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L. V.",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L.V",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L.V.",Louis Verchot: 0000-0001-8309-6754
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"Verchot, LV",Louis Verchot: 0000-0001-8309-6754
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"Verchot, Louis V.",Louis Verchot: 0000-0001-8309-6754
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"Mukankusi, Clare",Clare Mukankusi: 0000-0001-7837-4545
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"Mukankusi, Clare M.",Clare Mukankusi: 0000-0001-7837-4545
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"Wyckhuys, Kris",Kris Wyckhuys: 0000-0003-0922-488X
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"Wyckhuys, Kris A. G.",Kris Wyckhuys: 0000-0003-0922-488X
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"Wyckhuys, Kris A.G.",Kris Wyckhuys: 0000-0003-0922-488X
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"Chirinda, Ngonidzashe",Ngonidzashe Chirinda: 0000-0002-4213-6294
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"Chirinda, Ngoni",Ngonidzashe Chirinda: 0000-0002-4213-6294
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"Ngonidzashe, Chirinda",Ngonidzashe Chirinda: 0000-0002-4213-6294
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"Campbell, Bruce",Bruce M Campbell: 0000-0002-0123-4859
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"Campbell, Bruce M.",Bruce M Campbell: 0000-0002-0123-4859
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"Campbell, B.M",Bruce M Campbell: 0000-0002-0123-4859
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"Peters, Michael",Michael Peters: 0000-0003-4237-3916
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"Peters, M.",Michael Peters: 0000-0003-4237-3916
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"Peters, M.K.",Michael Peters: 0000-0003-4237-3916
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"Tamene, Lulseged",Lulseged Tamene: 0000-0002-3806-8890
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"Desta, Lulseged Tamene",Lulseged Tamene: 0000-0002-3806-8890
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"Läderach, Peter",Peter Läderach: 0000-0001-8708-6318
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"Lundy, Mark",Mark Lundy: 0000-0002-5241-3777
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"Schultze-Kraft, Rainer",Rainer Schultze-Kraft: 0000-0002-4563-0044
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"Schultze-Kraft, R.",Rainer Schultze-Kraft: 0000-0002-4563-0044
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"Verchot, Louis",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L. V.",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L.V",Louis Verchot: 0000-0001-8309-6754
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"Verchot, L.V.",Louis Verchot: 0000-0001-8309-6754
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"Verchot, LV",Louis Verchot: 0000-0001-8309-6754
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"Verchot, Louis V.",Louis Verchot: 0000-0001-8309-6754
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"Mukankusi, Clare",Clare Mukankusi: 0000-0001-7837-4545
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"Mukankusi, Clare M.",Clare Mukankusi: 0000-0001-7837-4545
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"Wyckhuys, Kris",Kris Wyckhuys: 0000-0003-0922-488X
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"Wyckhuys, Kris A. G.",Kris Wyckhuys: 0000-0003-0922-488X
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"Wyckhuys, Kris A.G.",Kris Wyckhuys: 0000-0003-0922-488X
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"Chirinda, Ngonidzashe",Ngonidzashe Chirinda: 0000-0002-4213-6294
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"Chirinda, Ngoni",Ngonidzashe Chirinda: 0000-0002-4213-6294
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"Ngonidzashe, Chirinda",Ngonidzashe Chirinda: 0000-0002-4213-6294
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</code></pre><ul>
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<li>The invocation would be:</li>
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</ul>
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<pre tabindex="0"><code>$ ./add-orcid-identifiers-csv.py -i 2018-08-16-ciat-orcid.csv -db dspace -u dspace -p 'fuuu'
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<pre tabindex="0"><code>$ ./add-orcid-identifiers-csv.py -i 2018-08-16-ciat-orcid.csv -db dspace -u dspace -p 'fuuu'
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</code></pre><ul>
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<li>I ran the script on DSpace Test and CGSpace and tagged a total of 986 ORCID identifiers</li>
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<li>Looking at the list of author affialitions from Peter one last time</li>
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@ -268,12 +268,12 @@ Verchot, Louis V.
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<li>This character all by itself is indicative of encoding issues in French, Italian, and Spanish names, for example: De´veloppement and Investigacio´n</li>
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<li>I will run the following on DSpace Test and CGSpace:</li>
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</ul>
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/2018-08-15-Correct-1083-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t correct -m 211
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$ ./delete-metadata-values.py -i /tmp/2018-08-15-Remove-11-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/2018-08-15-Correct-1083-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t correct -m 211
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$ ./delete-metadata-values.py -i /tmp/2018-08-15-Remove-11-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211
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</code></pre><ul>
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<li>Then force an update of the Discovery index on DSpace Test:</li>
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</ul>
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m"
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m"
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 72m12.570s
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@ -282,7 +282,7 @@ sys 2m2.461s
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</code></pre><ul>
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<li>And then on CGSpace:</li>
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</ul>
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
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<pre tabindex="0"><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 79m44.392s
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@ -292,9 +292,9 @@ sys 2m20.248s
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<li>Run system updates on DSpace Test and reboot the server</li>
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<li>In unrelated news, I see some newish Russian bot making a few thousand requests per day and not re-using its XMLUI session:</li>
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</ul>
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<pre tabindex="0"><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep '19/Aug/2018' | grep -c 5.9.6.51
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<pre tabindex="0"><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep '19/Aug/2018' | grep -c 5.9.6.51
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1553
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# grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=5.9.6.51' dspace.log.2018-08-19
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# grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=5.9.6.51' dspace.log.2018-08-19
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1724
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</code></pre><ul>
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<li>I don’t even know how its possible for the bot to use MORE sessions than total requests…</li>
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@ -391,11 +391,11 @@ $ dspace database migrate ignored
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<li>I exported a list of items from Listings and Reports with the following criteria: from year 2013 until now, have WLE subject <code>GENDER</code> or <code>GENDER POVERTY AND INSTITUTIONS</code>, and CRP <code>Water, Land and Ecosystems</code></li>
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<li>Then I extracted the Handle links from the report so I could export each item’s metadata as CSV</li>
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</ul>
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<pre tabindex="0"><code>$ grep -o -E "[0-9]{5}/[0-9]{0,5}" listings-export.txt > /tmp/iwmi-gender-items.txt
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<pre tabindex="0"><code>$ grep -o -E "[0-9]{5}/[0-9]{0,5}" listings-export.txt > /tmp/iwmi-gender-items.txt
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</code></pre><ul>
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<li>Then on the DSpace server I exported the metadata for each item one by one:</li>
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</ul>
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<pre tabindex="0"><code>$ while read -r line; do dspace metadata-export -f "/tmp/${line/\//-}.csv" -i $line; sleep 2; done < /tmp/iwmi-gender-items.txt
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<pre tabindex="0"><code>$ while read -r line; do dspace metadata-export -f "/tmp/${line/\//-}.csv" -i $line; sleep 2; done < /tmp/iwmi-gender-items.txt
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</code></pre><ul>
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<li>But from here I realized that each of the fifty-nine items will have different columns in their CSVs, making it difficult to combine them</li>
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<li>I’m not sure how to proceed without writing some script to parse and join the CSVs, and I don’t think it’s worth my time</li>
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