<li>Abenet said that CIP found more duplicate records in their export from AReS
<ul>
<li>I re-opened <ahref="https://github.com/ilri/OpenRXV/issues/67">the issue</a> on OpenRXV where we had previously noticed this</li>
<li>The shared link where the duplicates are is here: <ahref="https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6">https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6</a></li>
</ul>
</li>
<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
<li>Meeting with Peter and Abenet about CGSpace goals and progress</li>
<li>Test submission to DSpace via REST API to see if Abenet can fix / reject it (submit workflow?)</li>
<li>Get Peter a list of users who have submitted or approved on DSpace everrrrrrr, so he can remove some</li>
<li>Ask MEL for a dump of their types to reconcile with ours and CG Core</li>
<li>Need to tag ILRI collection with license!! For pre-2010 use “Other” unless a license is already there; 2010-2020 do the ilri content in batches (2010-2015: CC-BY-NC-SA; 2016-onwards: CC-BY);
<ul>
<li>ONLY if ILRI / International Livestock Research Institute is the publisher, no journal articles, no book chapters…</li>
</ul>
</li>
<li>I tried to export the ILRI community from CGSpace but I got an error:</li>
Exporting community 'International Livestock Research Institute (ILRI)' (10568/1)
Exception: null
java.lang.NullPointerException
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:212)
at com.google.common.collect.Iterators.concat(Iterators.java:464)
at org.dspace.app.bulkedit.MetadataExport.addItemsToResult(MetadataExport.java:136)
at org.dspace.app.bulkedit.MetadataExport.buildFromCommunity(MetadataExport.java:125)
at org.dspace.app.bulkedit.MetadataExport.<init>(MetadataExport.java:77)
at org.dspace.app.bulkedit.MetadataExport.main(MetadataExport.java:282)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>I imported the production database to my local development environment and I get the same error… WTF is this?
<ul>
<li>I was able to export another smaller community</li>
<li>I filed <ahref="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=919">an issue</a> with Atmire to see if it is likely something of theirs, or if I need to ask on the dspace-tech mailing list</li>
</ul>
</li>
<li>CodeObia sent a <ahref="https://github.com/ilri/OpenRXV/pull/71">pull request</a> with fixes for several issues we highlighted in OpenRXV
<ul>
<li>I deployed the fixes on production, as they only affect minor parts of the frontend, and two of the four are working</li>
<li>I sent feedback to CodeObia</li>
</ul>
</li>
</ul>
<h2id="2021-02-02">2021-02-02</h2>
<ul>
<li>Communicate more with CodeObia about some fixes for OpenRXV</li>
<li>Maria Garruccio sent me some new ORCID iDs for Bioversity authors, as well as a correction for Stefan Burkart’s iD</li>
<li>I saved the new ones to a text file, combined them with the others, extracted the ORCID iDs themselves, and updated the names using <code>resolve-orcids.py</code>:</li>
<li>Then for the rest, I saved them to a text file, combined them with the others, extracted the ORCID iDs themselves, and updated the names using <code>resolve-orcids.py</code>:</li>
<li>I also looked up which of these new authors might have existing items that are missing ORCID iDs</li>
<li>I had to port my <code>add-orcid-identifiers-csv.py</code> to DSpace 6 UUIDs and I think it’s working but I want to do a few more tests because it uses a sequence for the metadata_value_id</li>
</ul>
<h2id="2021-02-03">2021-02-03</h2>
<ul>
<li>Tag forty-three items from Bioversity’s new authors with ORCID iDs using <code>add-orcid-identifiers-csv.py</code>:</li>
<li>I’m working on the CGSpace accession for Karl Rich’s <ahref="https://github.com/ilri/vietnam-pig-model-2018">Viet Nam Pig Model 2018</a> and I noticed his ORCID iD is missing from CGSpace
<ul>
<li>I added it and tagged 141 items of his with the iD</li>
</ul>
</li>
<li>I <ahref="https://hdl.handle.net/10568/111126">uploaded a metadata-only accession</a> for the impact of ILRI book by John McIntire and Delia Grace to CGSpace
<ul>
<li>The source code itself is here: <ahref="https://github.com/ilri/impact-book">https://github.com/ilri/impact-book</a></li>
</ul>
</li>
<li>A little bit more work on CG Core v2</li>
</ul>
<h2id="2021-02-04">2021-02-04</h2>
<ul>
<li>Re-sync CGSpace database and Solr to DSpace Test to start a public test of CG Core v2
<ul>
<li>Afterwards I updated Discovery and OAI:</li>
</ul>
</li>
</ul>
<pre><codeclass="language-console"data-lang="console">$ time chrt -b 0 dspace index-discovery -b
$ dspace oai import -c
</code></pre><ul>
<li>Attend Accenture meeting for repository managers
<ul>
<li>Not clear what the SMO wants to get out of us</li>
</ul>
</li>
<li>Enrico asked for some notes about our work on AReS in 2020 for CRP Livestock reporting
<ul>
<li>Abenet and I came up with the following:</li>
</ul>
</li>
</ul>
<blockquote>
<p>In 2020 we funded the third phase of development on the OpenRXV platform that powers AReS. This phase focused mainly on improving the search filtering, graphical visualizations, and reporting capabilities. It is now possible to create custom reports in Excel, Word, and PDF formats using a templating system. We also concentrated on making the vanilla OpenRXV platform easier to deploy and administer in hopes that other organizations would begin using it. Lastly, we identified and fixed a handful of bugs in the system. All development takes place publicly on GitHub: <ahref="https://github.com/ilri/OpenRXV">https://github.com/ilri/OpenRXV</a>.</p>
</blockquote>
<blockquote>
<p>In the last quarter of 2020, ILRI conducted a briefing for nearly 100 scientists and communications staff on how to use ARes as a visualization tool for repository outputs and as a reporting tool (<ahref="https://hdl.handle.net/10568/110527)">https://hdl.handle.net/10568/110527)</a>. Staff will begin using AReS to generate lists of their outputs to upload in the performance evaluation system to assist in their performance evaluation. The list of publications they will upload from AReS to Performax will indicate the open access status of each publication to help start discussion why some outputs are not open access given the open access policies of the CGIAR.</p>
</blockquote>
<ul>
<li>Call Moayad to discuss OpenRXV development
<ul>
<li>We talked about the “reporting period” (date-based statistics) and some of the issues Abdullah is working on on GitHub</li>
<li>I suggested that we offer the date-range statistics in a modal dialog with other sorting and grouping options during report generation</li>
</ul>
</li>
<li>Peter sent me the cleaned up series that I had originally sent him in 2020-10
<ul>
<li>I quickly applied all the deletions on CGSpace:</li>
<li>Institutionalization of quality assurance mechanism and dissemination of top quality commercial products to increase crop yields and improve food security of smallholder farmers in sub-Saharan Africa – COMPRO-II</li>
<li>Manuel pour les Banques de Gènes;1</li>
<li>Sistematización de experiencias Proyecto ACORDAR</li>
<li>I ended up using <ahref="https://github.com/LuminosoInsight/python-ftfy">python-ftfy</a> to fix those very easily, then replaced them in the CSV</li>
<li>Then I trimmed whitespace at the beginning, end, and around the “;”, and applied the 1,600 fixes using <code>fix-metadata-values.py</code>:</li>
<li>Talk to Abdullah from CodeObia about a few of the issues we filed on OpenRXV
<ul>
<li>Verify a fix he made for the issue with spaces in template file names</li>
<li>He says that the <ahref="https://github.com/ilri/OpenRXV/issues/49">Angular expressions support should be enabled</a>, but I tried it and couldn’t get a few simple examples working</li>
</ul>
</li>
<li>Atmire responded to a few issues today:
<ul>
<li>First, the one about a crash while exporting a community CSV, which appears to be a <ahref="https://jira.lyrasis.org/browse/DS-4211">vanilla DSpace issue with a patch in DSpace 6.4</a></li>
<li>Second, the MQM batch consumer issue, which appears to be harmless log spam in <em>most</em> cases and they have sent a patch that adjusts the logging as such</li>
<li>Third, a version bump for CUA to fix the <code>java.lang.UnsupportedOperationException: Multiple update components target the same field:solr_update_time_stamp</code> error</li>
</ul>
</li>
<li>I cherry-picked the patches for DS-4111 and was able to export the ILRI community finally, but the results are almost twice as many items as in the community!
<ul>
<li>Investigating with csvcut I see there are some ids that appear up to five, six, or seven times!</li>
</ul>
</li>
</ul>
<pre><codeclass="language-console"data-lang="console">$ csvcut -c id /tmp/2021-02-10-ILRI.csv | sed '1d' | wc -l
30354
$ csvcut -c id /tmp/2021-02-10-ILRI.csv | sed '1d' | sort -u | wc -l
18555
$ csvcut -c id /tmp/2021-02-10-ILRI.csv | sed '1d' | sort | uniq -c | sort -h | tail
5 c21a79e5-e24e-4861-aa07-e06703d1deb7
5 c2460aa1-ae28-4003-9a99-2d7c5cd7fd38
5 d73fb3ae-9fac-4f7e-990f-e394f344246c
5 dc0e24fa-b7f5-437e-ac09-e15c0704be00
5 dc50bcca-0abf-473f-8770-69d5ab95cc33
5 e714bdf9-cc0f-4d9a-a808-d572e25c9238
6 7dfd1c61-9e8c-4677-8d41-e1c4b11d867d
6 fb76888c-03ae-4d53-b27d-87d7ca91371a
6 ff42d1e6-c489-492c-a40a-803cabd901ed
7 094e9e1d-09ff-40ca-a6b9-eca580936147
</code></pre><ul>
<li>I added a comment to that bug to ask if this is a side effect of the patch</li>
<li>I started working on tagging pre-2010 ILRI items with license information, like we talked about with Peter and Abenet last week
<ul>
<li>Due to the export bug I had to sort and remove duplicates first, then use csvgrep to filter out books and journal articles:</li>
<li>Run system updates, deploy latest <code>6_x-prod</code> branch, and reboot CGSpace (linode18)</li>
<li>Normalize <code>text_lang</code> of DSpace item metadata on CGSpace:</li>
</ul>
<pre><code>dspace=# SELECT DISTINCT text_lang, count(text_lang) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) GROUP BY text_lang ORDER BY count DESC;
text_lang | count
-----------+---------
en_US | 2567413
| 8050
en | 7601
| 0
(4 rows)
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id IN (SELECT uuid FROM item);
</code></pre><ul>
<li>Start a full Discovery re-indexing on CGSpace</li>
<li>Ah, actually 45.146.165.203 is making requests like this:</li>
</ul>
<pre><codeclass="language-console"data-lang="console">"http://cgspace.cgiar.org:80/bitstream/handle/10568/238/Res_report_no3.pdf;jsessionid=7311DD88B30EEF9A8F526FF89378C2C5%' AND 4313=CONCAT(CHAR(113)+CHAR(98)+CHAR(106)+CHAR(112)+CHAR(113),(SELECT (CASE WHEN (4313=4313) THEN CHAR(49) ELSE CHAR(48) END)),CHAR(113)+CHAR(106)+CHAR(98)+CHAR(112)+CHAR(113)) AND 'XzQO%'='XzQO"
</code></pre><ul>
<li>I purged the hits from these two using my <code>check-spider-ip-hits.sh</code>:</li>
Purging 27163 hits from 45.146.164.176 in statistics
Purging 19556 hits from 45.146.165.105 in statistics
Purging 15927 hits from 45.146.165.83 in statistics
Purging 8085 hits from 45.146.165.104 in statistics
Total number of bot hits purged: 70731
</code></pre><ul>
<li>My god, and 64.39.99.15 is from Qualys, the domain scanning security people, who are making queries trying to see if we are vulnerable or something (?)
<ul>
<li>Looking in Solr I see a few different IPs with DNS like <code>sn003.s02.iad01.qualys.com.</code> so I will purge their requests too:</li>
