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<meta property="og:title" content="September, 2020" />
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<meta property="og:description" content="2020-09-02
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Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS
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The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
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I restarted it again now and told Moayad that the automatic indexing isn’t working
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Add Alliance of Bioversity International and CIAT to affiliations on CGSpace
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Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
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I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
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I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
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<meta name="twitter:description" content="2020-09-02
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Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS
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The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
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I restarted it again now and told Moayad that the automatic indexing isn’t working
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Add Alliance of Bioversity International and CIAT to affiliations on CGSpace
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Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
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I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
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I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-09/">September, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-09-02T15:35:54+03:00">Wed Sep 02, 2020</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2020-09-02">2020-09-02</h2>
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<ul>
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<li>Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS</li>
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<li>The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
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<ul>
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<li>I restarted it again now and told Moayad that the automatic indexing isn’t working</li>
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</ul>
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</li>
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<li>Add <code>Alliance of Bioversity International and CIAT</code> to affiliations on CGSpace</li>
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<li>Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
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<ul>
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<li>I filed a bug on OpenRXV: <a href="https://github.com/ilri/OpenRXV/issues/39">https://github.com/ilri/OpenRXV/issues/39</a></li>
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</ul>
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</li>
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<li>I filed an issue on OpenRXV to make some minor edits to the admin UI: <a href="https://github.com/ilri/OpenRXV/issues/40">https://github.com/ilri/OpenRXV/issues/40</a></li>
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</ul>
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<ul>
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<li>I ran the country code tagger on CGSpace:</li>
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</ul>
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<pre><code>$ time chrt -b 0 dspace curate -t countrycodetagger -i all -r - -l 500 -s object | tee /tmp/2020-09-02-countrycodetagger.log
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...
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real 2m10.516s
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user 1m43.953s
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sys 0m15.192s
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$ grep -c added /tmp/2020-09-02-countrycodetagger.log
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39
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</code></pre><ul>
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<li>I still need to create a cron job for this…</li>
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<li>Sisay and Abenet said they can’t log in with LDAP on DSpace Test (DSpace 6)
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<ul>
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<li>I tried and I can’t either… but it is working on CGSpace</li>
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<li>The error on DSpace 6 is:</li>
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</ul>
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</li>
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</ul>
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<pre><code>2020-09-02 12:03:10,666 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=A629116488DCC467E1EA2062A2E2EFD7:ip_addr=92.220.02.201:failed_login:no DN found for user aorth
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</code></pre><ul>
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<li>I tried to query LDAP directly using the application credentials with ldapsearch and it works:</li>
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</ul>
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<pre><code>$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "applicationaccount@cgiarad.org" -W "(sAMAccountName=me)"
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</code></pre><ul>
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<li>According to the <a href="https://wiki.lyrasis.org/display/DSDOC6x/Authentication+Plugins#AuthenticationPlugins-LDAPAuthentication">DSpace 6 docs</a> we need to escape commas in our LDAP parameters due to the new configuration system
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<ul>
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<li>I added the commas and restarted DSpace (though technically we shouldn’t need to restart due to the new config system hot reloading configs)</li>
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<li>Run all system updates on DSpace Test (linode26) and reboot it</li>
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<li>After the restart LDAP login works…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-09-03">2020-09-03</h2>
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<ul>
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<li>Fix some erroneous “review status” fields that Abenet noticed on AReS
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<ul>
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<li>I used my <code>fix-metadata-values.py</code> and <code>delete-metadata-values.py</code> scripts with the following input files:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ cat 2020-09-03-fix-review-status.csv
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dc.description.version,correct
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Externally Peer Reviewed,Peer Review
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Peer Reviewed,Peer Review
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Peer review,Peer Review
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Peer reviewed,Peer Review
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Peer-Reviewed,Peer Review
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Peer-reviewed,Peer Review
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peer Review,Peer Review
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$ cat 2020-09-03-delete-review-status.csv
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dc.description.version
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Report
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Formally Published
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Poster
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Unrefereed reprint
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$ ./delete-metadata-values.py -i 2020-09-03-delete-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -m 68
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$ ./fix-metadata-values.py -i 2020-09-03-fix-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -t 'correct' -m 68
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</code></pre><ul>
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<li>Start reviewing 95 items for IITA (20201stbatch)
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<ul>
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<li>I used my <a href="https://github.com/ilri/csv-metadata-quality">csv-metadata-quality</a> tool to check and fix some low-hanging fruit first</li>
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<li>This fixed a few unnecessary Unicode, excessive whitespace, invalid multi-value separator, and duplicate metadata values</li>
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<li>Then I looked at the data in OpenRefine and noticed some things:
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<ul>
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<li>All issue dates use year only, but some have months in the citation so they could be more specific</li>
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<li>I normalized all the DOIs to use “<a href="https://doi.org">https://doi.org</a>” format</li>
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<li>I fixed a few AGROVOC subjects with a simple GREL: <code>value.replace("GRAINS","GRAIN").replace("SOILS","SOIL").replace("CORN","MAIZE")</code></li>
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<li>But there are a few more that are invalid that she will have to look at</li>
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<li>I uploaded the items to <a href="https://dspacetest.cgiar.org/handle/10568/108357">DSpace Test</a> and it was apparently successful but I get these errors to the console:</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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<pre><code>Thu Sep 03 12:26:33 CEST 2020 | Query:containerItem:ea7a2648-180d-4fce-bdc5-c3aa2304fc58
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Error while updating
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java.lang.NullPointerException
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1131)
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:212)
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1104)
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at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1093)
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at org.dspace.statistics.StatisticsLoggingConsumer.consume(SourceFile:104)
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at org.dspace.event.BasicDispatcher.consume(BasicDispatcher.java:177)
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at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:123)
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at org.dspace.core.Context.dispatchEvents(Context.java:455)
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at org.dspace.core.Context.commit(Context.java:424)
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at org.dspace.core.Context.complete(Context.java:380)
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at org.dspace.app.bulkedit.MetadataImport.main(MetadataImport.java:1399)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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</code></pre><ul>
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<li>There are more in the DSpace log so I will raise it with Atmire immediately</li>
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</ul>
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<h2 id="2020-09-04">2020-09-04</h2>
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<ul>
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<li>I was checking the recent IITA data for duplicates when I noticed that one in CIFOR’s Archive and saw that CIFOR has updated a bunch of their website URLs, for example:
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<ul>
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<li><a href="http://www.cifor.org/nc/online-library/browse/view-publication/publication/151.html">http://www.cifor.org/nc/online-library/browse/view-publication/publication/151.html</a> → <a href="https://www.cifor.org/knowledge/publication/151">https://www.cifor.org/knowledge/publication/151</a></li>
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<li><a href="https://www.cifor.org/library/4033">https://www.cifor.org/library/4033</a> → <a href="https://www.cifor.org/knowledge/publication/4033">https://www.cifor.org/knowledge/publication/4033</a></li>
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<li><a href="https://www.cifor.org/pid/5087">https://www.cifor.org/pid/5087</a> → <a href="https://www.cifor.org/knowledge/publication/5087">https://www.cifor.org/knowledge/publication/5087</a></li>
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</ul>
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</li>
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<li>I will update our nearly 6,000 metadata values for CIFOR in the database accordingly:</li>
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</ul>
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<pre><code>dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^(http://)?www\.cifor\.org/(nc/)?online-library/browse/view-publication/publication/([[:digit:]]+)\.html$', 'https://www.cifor.org/knowledge/publication/\3') WHERE metadata_field_id=219 AND text_value ~ 'www\.cifor\.org/(nc/)?online-library/browse/view-publication/publication/[[:digit:]]+';
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dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^https?://www\.cifor\.org/library/([[:digit:]]+)/?$', 'https://www.cifor.org/knowledge/publication/\1') WHERE metadata_field_id=219 AND text_value ~ 'https?://www\.cifor\.org/library/[[:digit:]]+/?';
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dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^https?://www\.cifor\.org/pid/([[:digit:]]+)/?$', 'https://www.cifor.org/knowledge/publication/\1') WHERE metadata_field_id=219 AND text_value ~ 'https?://www\.cifor\.org/pid/[[:digit:]]+';
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</code></pre><ul>
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<li>I did some cleanup on the author affiliations of the IITA data our 2019-04 list using reconcile-csv and OpenRefine:
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<ul>
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<li><code>$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id</code></li>
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<li>I always forget how to copy the reconciled values in OpenRefine, but you need to make a new column and populate it using this GREL: <code>if(cell.recon.matched, cell.recon.match.name, value)</code></li>
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</ul>
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</li>
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<li>I mapped one duplicated from the CIFOR Archives and re-uploaded the 94 IITA items to a new collection on <a href="https://dspacetest.cgiar.org/handle/10568/108453">DSpace Test</a></li>
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</ul>
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<h2 id="2020-09-08">2020-09-08</h2>
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<ul>
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<li>I noticed that the “share” link in AReS wasn’t working properly because it excludes the “explorer” part of the URI</li>
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</ul>
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<p><img src="/cgspace-notes/2020/09/ares-share-link.png" alt="AReS share link broken"></p>
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<ul>
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<li>I filed an issue on GitHub: <a href="https://github.com/ilri/OpenRXV/issues/41">https://github.com/ilri/OpenRXV/issues/41</a></li>
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<li>I uploaded the 94 IITA items that I had been working on last week to CGSpace</li>
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<li>RTB emailed to ask why they are getting HTTP 503 errors during harvesting to the RTB WordPress website
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<ul>
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<li>From the screenshot I can see they are requesting URLs like this:</li>
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</ul>
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</li>
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</ul>
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<pre><code>https://cgspace.cgiar.org/bitstream/handle/10568/82745/Characteristics-Silage.JPG
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</code></pre><ul>
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<li>So they end up getting rate limited due to the XMLUI rate limits
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<ul>
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<li>I told them to use the REST API bitstream retrieve links, because we don’t have any rate limits there</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-09-09">2020-09-09</h2>
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<ul>
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<li>Wire up the systemd service/timer for the CGSpace Country Code Tagger curation task in the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a>
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<ul>
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<li><del>For now it won’t work on DSpace 6 because the curation task invocation needs to be slightly different (minus the <code>-l</code> parameter) and for some reason the task isn’t working on DSpace Test (version 6) right now</del></li>
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<li>I added DSpace 6 support to the playbook templates…</li>
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</ul>
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</li>
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<li>Run system updates on DSpace Test (linode26), re-deploy the DSpace 6 test branch, and reboot the server
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<ul>
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<li>After rebooting I deleted old copies of the cgspace-java-helpers JAR in the DSpace lib directory and then the curation worked</li>
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<li>To my great surprise the curation worked (and completed, albeit a few times slower) on my local DSpace 6 environment as well:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ ~/dspace63/bin/dspace curate -t countrycodetagger -i all -s object
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</code></pre><h2 id="2020-09-10">2020-09-10</h2>
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<ul>
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<li>I checked the country code tagger on CGSpace and DSpace Test and it ran fine from the systemd timer last night… w00t</li>
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<li>I started looking at Peter’s changes to the CGSpace regions that were proposed in 2020-07
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<ul>
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<li>The changes will be:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ cat 2020-09-10-fix-cgspace-regions.csv
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cg.coverage.region,correct
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EAST AFRICA,EASTERN AFRICA
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WEST AFRICA,WESTERN AFRICA
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SOUTHEAST ASIA,SOUTHEASTERN ASIA
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SOUTH ASIA,SOUTHERN ASIA
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AFRICA SOUTH OF SAHARA,SUB-SAHARAN AFRICA
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NORTH AFRICA,NORTHERN AFRICA
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WEST ASIA,WESTERN ASIA
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SOUTHWEST ASIA,SOUTHWESTERN ASIA
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$ ./fix-metadata-values.py -i 2020-09-10-fix-cgspace-regions.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.region -t 'correct' -m 227 -d -n
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Connected to database.
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Would fix 12227 occurences of: EAST AFRICA
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Would fix 7996 occurences of: WEST AFRICA
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Would fix 3515 occurences of: SOUTHEAST ASIA
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Would fix 3443 occurences of: SOUTH ASIA
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Would fix 1134 occurences of: AFRICA SOUTH OF SAHARA
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Would fix 357 occurences of: NORTH AFRICA
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Would fix 81 occurences of: WEST ASIA
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Would fix 3 occurences of: SOUTHWEST ASIA
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</code></pre><ul>
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<li>I think we need to wait for the web team, though, as they need to update their mappings
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<ul>
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<li>Not to mention that we’ll need to give WLE and CCAFS time to update their harvesters as well… hmmm</li>
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</ul>
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</li>
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<li>Looking at the top user agents active on CGSpace in 2020-08 and I see:
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<ul>
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<li><code>Delphi 2009</code>: 235353 (this is GARDIAN harvester I guess, as the IP is in Greece)</li>
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<li><code>Mozilla/4.5 (compatible; HTTrack 3.0x; Windows 98)</code>: 57004 (IP is 18.196.100.94, and the requests seem to be for CTA’s content)</li>
|
|
<li><code>RTB website BOT</code>: 12282</li>
|
|
<li><code>ILRI Livestock Website Publications importer BOT</code>: 9393</li>
|
|
</ul>
|
|
</li>
|
|
<li>Shit, I meant to add Delphi to the DSpace spider agents list last month but I guess I didn’t commit the change</li>
|
|
<li>HTTrack is in the agents list so I’m not sure why DSpace registers a hit from that request</li>
|
|
<li>Also, I am surprised to see the RTB and ILRI bots here because they have “BOT” in the name and that should also be dropped</li>
|
|
<li>I also see hits from <code>curl</code> and <code>Java/1.8.0_66</code> and <code>Apache-HttpClient</code> so WTF… those are supposed to be dropped by the default agents list</li>
|
|
<li>Some IP <code>2607:f298:5:101d:f816:3eff:fed9:a484</code> made 9,000 requests with the <code>RI/1.0</code> user agent this year…
|
|
<ul>
|
|
<li>That’s on DreamHost…?</li>
|
|
</ul>
|
|
</li>
|
|
<li>I purged 448658 hits from these agents and added <code>Delphi</code> to our local agents overload for Solr as well as Tomcat’s Crawler Session Manager Valve so that it forces them to re-use a single session</li>
|
|
<li>I made a pull request on the COUNTER-Robots project for the Daum robot: <a href="https://github.com/atmire/COUNTER-Robots/pull/38">https://github.com/atmire/COUNTER-Robots/pull/38</a>
|
|
<ul>
|
|
<li>This bot made 8,000 requests to CGSpace this year</li>
|
|
<li>I purged about 20,000 total requests from this bot from our Solr stats for the last few years</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-09-11">2020-09-11</h2>
|
|
<ul>
|
|
<li>Peter noticed that an export from AReS shows some items with zero views and others with zero views/downloads, but on CGSpace and in the statistics API there are views/downloads
|
|
<ul>
|
|
<li>I need to ask Moayad…</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-09-12">2020-09-12</h2>
|
|
<ul>
|
|
<li>Carlos Tejo from the LandPortal emailed to ask for advice about integrating their <a href="https://landvoc.org/">LandVoc</a> vocabulary, which is a subset of AGROVOC, into DSpace
|
|
<ul>
|
|
<li>I told him that they could use the DSpace authority control framework and sent an example of the VIAFAuthority from the DSpace-CRIS project: <a href="https://github.com/4Science/DSpace/blob/dspace-6_x_x-cris/dspace-api/src/main/java/org/dspace/content/authority/VIAFAuthority.java">https://github.com/4Science/DSpace/blob/dspace-6_x_x-cris/dspace-api/src/main/java/org/dspace/content/authority/VIAFAuthority.java</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Redeploy the latest <code>5_x-prod</code> branch on CGSpace, re-run the latest Ansible DSpace playbook, run all system updates, and reboot the server (linode18)
|
|
<ul>
|
|
<li>This will bring the latest bot lists for Solr and Tomcat</li>
|
|
<li>I had to restart Tomcat 7 three times before all Solr statistics cores came up OK</li>
|
|
</ul>
|
|
</li>
|
|
<li>Leroy and Carol from CIAT/Bioversity were asking for information about posting to the CGSpace REST API from Sharepoint
|
|
<ul>
|
|
<li>I told them that we don’t allow this yet, but that we need to check in the future whether content can be posted to a workflow</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-09-15">2020-09-15</h2>
|
|
<ul>
|
|
<li>Charlotte from Altmetric said they had issues parsing the XML file I sent them last month
|
|
<ul>
|
|
<li>I told them that it was mimicking the same format that they had sent me (fourteen pages of XML responses concatenated together)!</li>
|
|
</ul>
|
|
</li>
|
|
<li>A few days ago IWMI asked us if we can add a new field on CGSpace for their library identifier
|
|
<ul>
|
|
<li>The IDs look like this: H049940</li>
|
|
<li>I suggested that we use <code>cg.identifier.iwmilibrary</code></li>
|
|
<li>I added it to the input forms and push it to the <code>5_x-prod</code> and 6.x branches and will re-deploy it in the next few days</li>
|
|
</ul>
|
|
</li>
|
|
<li>Abenet asked me to import sixty-nine (69) CIP Annual Reports to CGSpace
|
|
<ul>
|
|
<li>I looked at the data in OpenRefine and it is very good quality</li>
|
|
<li>I only added descriptions to the filename field so that SAFBuilder will add them to the bitstreams on import:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>value + "__description:" + cells["dc.type"].value
|
|
</code></pre><ul>
|
|
<li>Then I created a SAF bundle with SAFBuilder:</li>
|
|
</ul>
|
|
<pre><code>$ ./safbuilder.sh -c ~/Downloads/cip-annual-reports/cip-reports.csv
|
|
</code></pre><ul>
|
|
<li>And imported them into my local test instance of CGSpace:</li>
|
|
</ul>
|
|
<pre><code>$ ~/dspace/bin/dspace import -a -e y.arrr@cgiar.org -m /tmp/2020-09-15-cip-annual-reports.map -s ~/Downloads/cip-annual-reports/SimpleArchiveFormat
|
|
</code></pre><ul>
|
|
<li>Then I uploaded them to CGSpace</li>
|
|
</ul>
|
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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|
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|
|
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
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|
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<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
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|
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<li><a href="/cgspace-notes/2020-07/">July, 2020</a></li>
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<li><a href="/cgspace-notes/2020-06/">June, 2020</a></li>
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<li><a href="/cgspace-notes/2020-05/">May, 2020</a></li>
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</ol>
|
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</section>
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|
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<section class="sidebar-module">
|
|
<h4>Links</h4>
|
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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>
|
|
|
|
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
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|
|
</ol>
|
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</section>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p dir="auto">
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