<li>Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK</li>
<li>I manually installed OpenJDK, then removed Oracle JDK, then re-ran the <ahref="http://github.com/ilri/rmg-ansible-public">Ansible playbook</a> to update all configuration files, etc</li>
<li>Then I ran all system updates and restarted the server</li>
</ul>
<h2id="2018-12-02">2018-12-02</h2>
<ul>
<li>I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another <ahref="https://usn.ubuntu.com/3831-1/">Ghostscript vulnerability last week</a></li>
</ul>
<ul>
<li>The error when I try to manually run the media filter for one item from the command line:</li>
at org.im4java.core.Info.getBaseInfo(Info.java:360)
at org.im4java.core.Info.<init>(Info.java:151)
at org.dspace.app.mediafilter.ImageMagickThumbnailFilter.getImageFile(ImageMagickThumbnailFilter.java:142)
at org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.getDestinationStream(ImageMagickPdfThumbnailFilter.java:24)
at org.dspace.app.mediafilter.FormatFilter.processBitstream(FormatFilter.java:170)
at org.dspace.app.mediafilter.MediaFilterManager.filterBitstream(MediaFilterManager.java:475)
at org.dspace.app.mediafilter.MediaFilterManager.filterItem(MediaFilterManager.java:429)
at org.dspace.app.mediafilter.MediaFilterManager.applyFiltersItem(MediaFilterManager.java:401)
at org.dspace.app.mediafilter.MediaFilterManager.main(MediaFilterManager.java:237)
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:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
</code></pre>
<ul>
<li>A comment on <ahref="https://stackoverflow.com/questions/53560755/ghostscript-9-26-update-breaks-imagick-readimage-for-multipage-pdf">StackOverflow question</a> from yesterday suggests it might be a bug with the <code>pngalpha</code> device in Ghostscript and <ahref="https://bugs.ghostscript.com/show_bug.cgi?id=699815">links to an upstream bug</a></li>
<li>I think we need to wait for a fix from Ubuntu</li>
<li>Start proofing the latest round of 226 IITA archive records that Bosede sent last week and Sisay uploaded to DSpace Test this weekend (<ahref="https://dspacetest.cgiar.org/handle/10568/108298">IITA_Dec_1_1997 aka Daniel1807</a>)
<ul>
<li>One item missing the authorship type</li>
<li>Some invalid countries (smart quotes, mispellings)</li>
<li>Added countries to some items that mentioned research in particular countries in their abstracts</li>
<li>One item had “MADAGASCAR” for ISI Journal</li>
<li>Minor corrections in IITA subject (LIVELIHOOD→LIVELIHOODS)</li>
<li>Trim whitespace in abstract field</li>
<li>Fix some sponsors (though some with “Governments of Canada” etc I’m not sure why those are plural)</li>
<li>Eighteen items had <code>en||fr</code> for the language, but the content was only in French so changed them to just <code>fr</code></li>
<li>Six items had encoding errors in French text so I will ask Bosede to re-do them carefully</li>
<li>Correct and normalize a few AGROVOC subjects</li>
</ul></li>
<li>Expand my “encoding error” detection GREL to include <code>~</code> as I saw a lot of that in some copy pasted French text recently:</li>
<li>I looked at the DSpace Ghostscript issue more and it seems to only affect certain PDFs…</li>
<li>I can successfully generate a thumbnail for another recent item (<ahref="https://hdl.handle.net/10568/98394"><sup>10568</sup>⁄<sub>98394</sub></a>), but not for <ahref="https://hdl.handle.net/10568/98390"><sup>10568</sup>⁄<sub>98930</sub></a></li>
<li>Even manually on my Arch Linux desktop with ghostscript 9.26-1 and the <code>pngalpha</code> device, I can generate a thumbnail for the first one (<sup>10568</sup>⁄<sub>98394</sub>):</li>
Info Note Mainstreaming gender and social differentiation into CCAFS research activities in West Africa-converted.pdf[0]=>Info Note Mainstreaming gender and social differentiation into CCAFS research activities in West Africa-converted.pdf PDF 595x841 595x841+0+0 16-bit sRGB 107443B 0.000u 0:00.000
<li>And wow, I can’t even run ImageMagick’s <code>identify</code> on the first page of the second item (<sup>10568</sup>⁄<sub>98930</sub>):</li>
Food safety Kenya fruits.pdf PDF 612x792+0+0 DirectClass 8-bit 1.4Mi 0.000u 0m:0.000002s
</code></pre>
<ul>
<li>Interesting that ImageMagick’s <code>identify</code><em>does</em> work if you do not specify a page, perhaps as <ahref="https://bugs.ghostscript.com/show_bug.cgi?id=699815">alluded to in the recent Ghostscript bug report</a>:</li>
<li>I inspected the troublesome PDF using <ahref="http://jhove.openpreservation.org/">jhove</a> and noticed that it is using <code>ISO PDF/A-1, Level B</code> and the other one doesn’t list a profile, though I don’t think this is relevant</li>
<li>I found another item that fails when generating a thumbnail (<ahref="https://hdl.handle.net/10568/98391"><sup>10568</sup>⁄<sub>98391</sub></a>, DSpace complains:</li>
<li>I’ve tried a few times this week to register for the <ahref="https://www.evisa.gov.et/">Ethiopian eVisa website</a>, but it is never successful</li>
<li>In the end I tried one last time to just apply without registering and it was apparently successful</li>
<li>Testing DSpace 5.8 (<code>5_x-prod</code> branch) in an Ubuntu 18.04 VM with Tomcat 8.5 and had some issues:
<ul>
<li>JSPUI shows an internal error (log shows something about tag cloud, though, so might be unrelated)</li>
<li>Atmire Listings and Reports, which use JSPUI, asks you to log in again and then doesn’t work</li>
<li>Content and Usage Analysis doesn’t show up in the sidebar after logging in</li>
<li>I can navigate to <ahref="https://dspacetest.cgiar.org/atmire/reporting-suite/usage-graph-editor">/atmire/reporting-suite/usage-graph-editor</a>, but it’s only the Atmire theme and a “page not found” message</li>
<li>Related messages from dspace.log:</li>
</ul></li>
</ul>
<pre><code>2018-12-03 15:44:00,030 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2018-12-03 15:45:01,667 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-listing-and-reports not found
</code></pre>
<ul>
<li>I tested it on my local environment with Tomcat 8.5.34 and the JSPUI application still has an error (again, the logs show something about tag cloud, so be unrelated), and the Listings and Reports still asks you to log in again, despite already being logged in in XMLUI, but does appear to work (I generated a report and exported a PDF)</li>
<li>I think the errors about missing Atmire components must be important, here on my local machine as well (though not the one about atmire-listings-and-reports):</li>
</ul>
<pre><code>2018-12-03 16:44:00,009 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
</code></pre>
<ul>
<li>This has got to be part Ubuntu Tomcat packaging, and part DSpace 5.x Tomcat 8.5 readiness…?</li>
<li>Last night Linode sent a message that the load on CGSpace (linode18) was too high, here’s a list of the top users at the time and throughout the day:</li>
<li><code>35.237.175.180</code> is known to us (CCAFS?), and I’ve already added it to the list of bot IPs in nginx, which appears to be working:</li>
<li>In other news, it’s good to see my re-work of the database connectivity in the <ahref="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> actually caused a reduction of persistent database connections (from 1 to 0, but still!):</li>
<li>We came up with an <ahref="https://cgspace.cgiar.org/open-search/discover?query=crpsubject:Water,+Land+and+Ecosystems&sort_by=3&order=DESC">OpenSearch query for all items tagged with the WLE CRP subject</a> (where the <code>sort_by=3</code> parameter is the accession date, as configured in <code>dspace.cfg</code>)</li>
<li>About Altmetric she was wondering why some low-ranking items of theirs do not have the Handle/DOI relationship, but high-ranking ones do</li>
<li>It sounds kinda crazy, but she said when she talked to Altmetric about their Twitter harvesting they said their coverage is not perfect, so it might be some kinda prioritization thing where they only do it for popular items?</li>
<li>I am testing this by <ahref="https://twitter.com/mralanorth/status/1072153586342211584">tweeting</a> one <ahref="https://cgspace.cgiar.org/handle/10568/98380">WLE item from CGSpace</a> that currently has no Altmetric score</li>
<li>Interestingly, after about an hour I see it has already been <ahref="https://cgspace.altmetric.com/details/50160871/twitter">picked up by Altmetric</a> and has my tweet as well as some other tweet from over a month ago…</li>
<li>I <ahref="https://twitter.com/mralanorth/status/1072198292182892545">tweeted a link to the item’s DOI</a> to see if Altmetric will notice it, hopefully associated with the Handle I tweeted earlier</li>
<li>I checked the <ahref="https://twitter.com/mralanorth/status/1072198292182892545">latest tweet of the IWMI item with a DOI</a> and it was <ahref="https://cgspace.altmetric.com/details/50160871/twitter">picked up by Altmetric</a>
<ul>
<li>There is one <ahref="twitter.com/ArboNews/statuses/1055036747787223042">curious other tweet</a> from another user where they used the NCBI link, and that is also associated with our Handle on Altmetric</li>
<li>So that means Altmetric is picking up the DOI from the NCBI metadata and making the association properly</li>
<li><code>94.71.244.172</code> and <code>143.233.227.216</code> are both in Greece and use the following user agent:</li>
</ul>
<pre><code>Mozilla/3.0 (compatible; Indy Library)
</code></pre>
<ul>
<li>I see that I added this bot to the Tomcat Crawler Session Manager valve in 2017-12 so its XMLUI sessions are getting re-used</li>
<li><code>2a01:4f8:173:1e85::2</code> is some new bot called <code>BLEXBot/1.0</code> which should be matching the existing “bot” pattern in the Tomcat Crawler Session Manager regex</li>
<li>Open a <ahref="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=657">ticket</a> with Atmire to ask them to prepare the Metadata Quality Module for our DSpace 5.8 code</li>
<li>Update Atmire Listings and Reports to add the journal title (<code>dc.source</code>) to bibliography and update example bibliography values (<ahref="https://github.com/ilri/DSpace/pull/405">#405</a>)</li>
<li>Peter pointed out that Discovery filters for CTA subjects on item pages were not working</li>
<li>It looks like there were some mismatches in the Discovery index names and the XMLUI configuration, so I fixed them (<ahref="https://github.com/ilri/DSpace/pull/406">#406</a>)</li>
<li>Peter asked if we could create a controlled vocabulary for publishers (<code>dc.publisher</code>)</li>
<li>I see we have about 3500 distinct publishers:</li>
</ul>
<pre><code># SELECT COUNT(DISTINCT(text_value)) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=39;
count
-------
3522
(1 row)
</code></pre>
<ul>
<li>I reverted the metadata changes related to “Unrestricted Access” and “Restricted Access” on DSpace Test because we’re not pushing forward with the new status terms for now</li>
<li>Purge remaining Oracle Java 8 stuff from CGSpace (linode18) since we migrated to OpenJDK a few months ago:</li>
