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Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK
I manually installed OpenJDK, then removed Oracle JDK, then re-ran the Ansible playbook to update all configuration files, etc
Then I ran all system updates and restarted the server
2018-12-02
I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week
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Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK
I manually installed OpenJDK, then removed Oracle JDK, then re-ran the Ansible playbook to update all configuration files, etc
Then I ran all system updates and restarted the server
2018-12-02
I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-12/">December, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-12-02T02:09:30&#43;02:00">Sun Dec 02, 2018</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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<h2 id="2018-12-01">2018-12-01</h2>
<ul>
<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 <a href="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>
<h2 id="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 <a href="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>
</ul>
<pre><code>org.im4java.core.InfoException: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: FailedToExecuteCommand `&quot;gs&quot; -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 &quot;-sDEVICE=pngalpha&quot; -dTextAlphaBits=4 -dGraphicsAlphaBits=4 &quot;-r72x72&quot; -dFirstPage=1 -dLastPage=1 &quot;-sOutputFile=/tmp/magick-12989PcFN0DnJOej7%d&quot; &quot;-f/tmp/magick-129895Bmp44lvUfxo&quot; &quot;-f/tmp/magick-12989C0QFG51fktLF&quot;' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
org.im4java.core.InfoException: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: FailedToExecuteCommand `&quot;gs&quot; -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 &quot;-sDEVICE=pngalpha&quot; -dTextAlphaBits=4 -dGraphicsAlphaBits=4 &quot;-r72x72&quot; -dFirstPage=1 -dLastPage=1 &quot;-sOutputFile=/tmp/magick-12989PcFN0DnJOej7%d&quot; &quot;-f/tmp/magick-129895Bmp44lvUfxo&quot; &quot;-f/tmp/magick-12989C0QFG51fktLF&quot;' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
at org.im4java.core.Info.getBaseInfo(Info.java:360)
at org.im4java.core.Info.&lt;init&gt;(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 <a href="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 <a href="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>
Update notes for 2018-12-02
2018-12-02 09:57:41 +01:00
<li>For what it&rsquo;s worth, I get the same error on my local Arch Linux environment with Ghostscript 9.26:</li>
Add notes for 2018-12-02
2018-12-02 09:47:41 +01:00
</ul>
Update notes for 2018-12-02
2018-12-02 09:57:41 +01:00
<pre><code>$ gs -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 -sDEVICE=pngalpha -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r72x72 -dFirstPage=1 -dLastPage=1 -sOutputFile=/tmp/out%d -f/home/aorth/Desktop/Food\ safety\ Kenya\ fruits.pdf
DEBUG: FC_WEIGHT didn't match
zsh: segmentation fault (core dumped) gs -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000
</code></pre>
<ul>
<li>When I replace the <code>pngalpha</code> device with <code>png16m</code> as suggested in the StackOverflow comments it works:</li>
</ul>
<pre><code>$ gs -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 -sDEVICE=png16m -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r72x72 -dFirstPage=1 -dLastPage=1 -sOutputFile=/tmp/out%d -f/home/aorth/Desktop/Food\ safety\ Kenya\ fruits.pdf
DEBUG: FC_WEIGHT didn't match
</code></pre>
Update notes for 2018-12-02
2018-12-02 16:55:32 +01:00
<ul>
<li>Start proofing the latest round of 226 IITA archive records that Bosede sent last week and Sisay uploaded to DSpace Test this weekend (<a href="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 &ldquo;MADAGASCAR&rdquo; 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 &ldquo;Governments of Canada&rdquo; etc I&rsquo;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 &ldquo;encoding error&rdquo; detection GREL to include <code>~</code> as I saw a lot of that in some copy pasted French text recently:</li>
</ul>
<pre><code>or(
isNotNull(value.match(/.*\uFFFD.*/)),
isNotNull(value.match(/.*\u00A0.*/)),
isNotNull(value.match(/.*\u200A.*/)),
isNotNull(value.match(/.*\u2019.*/)),
isNotNull(value.match(/.*\u00b4.*/)),
isNotNull(value.match(/.*\u007e.*/))
)
</code></pre>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2018-12/">December, 2018</a></li>
<li><a href="/cgspace-notes/2018-11/">November, 2018</a></li>
<li><a href="/cgspace-notes/2018-10/">October, 2018</a></li>
<li><a href="/cgspace-notes/2018-09/">September, 2018</a></li>
<li><a href="/cgspace-notes/2018-08/">August, 2018</a></li>
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