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Run the 279 CIAT author corrections on CGSpace


2017-03-02


Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
They might come in at the top level in one &ldquo;CGIAR System&rdquo; community, or with several communities
I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?
Need to send Peter and Michael some notes about this in a few days
Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
Filed an issue on DSpace issue tracker for the filter-media bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: DS-3516
Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing regeneration using DSpace 5.x&rsquo;s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see 10568&frasl;51999):


$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600&#43;0&#43;0 8-bit CMYK 168KB 0.000u 0:00.000


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Run the 279 CIAT author corrections on CGSpace


2017-03-02


Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
They might come in at the top level in one &ldquo;CGIAR System&rdquo; community, or with several communities
I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?
Need to send Peter and Michael some notes about this in a few days
Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
Filed an issue on DSpace issue tracker for the filter-media bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: DS-3516
Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing regeneration using DSpace 5.x&rsquo;s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see 10568&frasl;51999):


$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600&#43;0&#43;0 8-bit CMYK 168KB 0.000u 0:00.000


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<article class="blog-post">
  <header>
    <h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-03/">March, 2017</a></h2>
    <p class="blog-post-meta"><time datetime="2017-03-01T17:08:52&#43;02:00">Wed Mar 01, 2017</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>

</p>
  </header>
  <h2 id="2017-03-01">2017-03-01</h2>

<ul>
<li>Run the 279 CIAT author corrections on CGSpace</li>
</ul>

<h2 id="2017-03-02">2017-03-02</h2>

<ul>
<li>Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace</li>
<li>CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles</li>
<li>They might come in at the top level in one &ldquo;CGIAR System&rdquo; community, or with several communities</li>
<li>I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?</li>
<li>Need to send Peter and Michael some notes about this in a few days</li>
<li>Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI</li>
<li>Filed an issue on DSpace issue tracker for the <code>filter-media</code> bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: <a href="https://jira.duraspace.org/browse/DS-3516">DS-3516</a></li>
<li>Discovered that the ImageMagic <code>filter-media</code> plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK</li>
<li>Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing regeneration using DSpace 5.x&rsquo;s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see <a href="https://cgspace.cgiar.org/handle/10568/51999"><sup>10568</sup>&frasl;<sub>51999</sub></a>):</li>
</ul>

<pre><code>$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
</code></pre>

<p></p>

<ul>
<li>This results in discolored thumbnails when compared to the original PDF, for example sRGB and CMYK:</li>
</ul>

<p><img src="/cgspace-notes/2017/03/thumbnail-srgb.jpg" alt="Thumbnail in sRGB colorspace" /></p>

<p><img src="/cgspace-notes/2017/03/thumbnail-cmyk.jpg" alt="Thumbnial in CMYK colorspace" /></p>

<ul>
<li>I filed an issue for the color space thing: <a href="https://jira.duraspace.org/browse/DS-3517">DS-3517</a></li>
</ul>

<h2 id="2017-03-03">2017-03-03</h2>

<ul>
<li>I created a patch for DS-3517 and made a pull request against upstream <code>dspace-5_x</code>: <a href="https://github.com/DSpace/DSpace/pull/1669">https://github.com/DSpace/DSpace/pull/1669</a></li>
<li>Looks like <code>-colorspace sRGB</code> alone isn&rsquo;t enough, we need to use profiles:</li>
</ul>

<pre><code>$ convert alc_contrastes_desafios.pdf\[0\] -profile /opt/brew/Cellar/ghostscript/9.20/share/ghostscript/9.20/iccprofiles/default_cmyk.icc -thumbnail 300x300 -flatten -profile /opt/brew/Cellar/ghostscript/9.20/share/ghostscript/9.20/iccprofiles/default_rgb.icc alc_contrastes_desafios.pdf.jpg
</code></pre>

<ul>
<li>This reads the input file, applies the CMYK profile, applies the RGB profile, then writes the file</li>
<li>Note that you should set the first profile immediately after the input file</li>
<li>Also, it is better to use profiles than setting <code>-colorspace</code></li>
<li>This is a great resource describing the color stuff: <a href="http://www.imagemagick.org/Usage/formats/#profiles">http://www.imagemagick.org/Usage/formats/#profiles</a></li>
<li>Somehow we need to detect the color system being used by the input file and handle each case differently (with profiles)</li>
<li>This is trivial with <code>identify</code> (even by the <a href="http://im4java.sourceforge.net/api/org/im4java/core/IMOps.html#identify">Java ImageMagick API</a>):</li>
</ul>

<pre><code>$ identify -format '%r\n' alc_contrastes_desafios.pdf\[0\]
DirectClass CMYK
$ identify -format '%r\n' Africa\ group\ of\ negotiators.pdf\[0\]
DirectClass sRGB Alpha
</code></pre>

<h2 id="2017-03-05">2017-03-05</h2>

<ul>
<li>Look into helping developers from landportal.info with a query for items related to LAND on the REST API</li>
<li>They want something like the items that are returned by the general &ldquo;LAND&rdquo; query in the search interface, but we cannot do that</li>
<li>We can only return specific results for metadata fields, like:</li>
</ul>

<pre><code>$ curl -s -H &quot;accept: application/json&quot; -H &quot;Content-Type: application/json&quot; -X POST &quot;https://dspacetest.cgiar.org/rest/items/find-by-metadata-field&quot; -d '{&quot;key&quot;: &quot;cg.subject.ilri&quot;,&quot;value&quot;: &quot;LAND REFORM&quot;, &quot;language&quot;: null}' | json_pp
</code></pre>

<ul>
<li>But there are hundreds of combinations of fields and values (like <code>dc.subject</code> and all the center subjects), and we can&rsquo;t use wildcards in REST!</li>
</ul>

  
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			`Run the 279 CIAT author corrections on CGSpace`


Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`2017-03-02`


Update notes for 2017-03-03 2017-03-04 00:15:47 +01:00			`Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace`
			`CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles`
			`They might come in at the top level in one “CGIAR System” community, or with several communities`
			`I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?`
			`Need to send Peter and Michael some notes about this in a few days`
			`Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI`
Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`Filed an issue on DSpace issue tracker for the filter-media bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: DS-3516`
			`Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK`
			`Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see 10568&frasl;51999):`


			`$ identify ~/Desktop/alc_contrastes_desafios.jpg`
			`/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000`


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			`Run the 279 CIAT author corrections on CGSpace`


Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`2017-03-02`


Update notes for 2017-03-03 2017-03-04 00:15:47 +01:00			`Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace`
			`CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles`
			`They might come in at the top level in one “CGIAR System” community, or with several communities`
			`I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?`
			`Need to send Peter and Michael some notes about this in a few days`
			`Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI`
Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`Filed an issue on DSpace issue tracker for the filter-media bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: DS-3516`
			`Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK`
			`Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see 10568&frasl;51999):`


			`$ identify ~/Desktop/alc_contrastes_desafios.jpg`
			`/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000`


Add notes for 2017-03-01 2017-03-01 16:10:08 +01:00			`"/>`

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			`<p class="blog-post-meta"><time datetime="2017-03-01T17:08:52+02:00">Wed Mar 01, 2017</time> by Alan Orth in`

			`<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>`

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			`</header>`
			`<h2 id="2017-03-01">2017-03-01</h2>`

			`<ul>`
			`<li>Run the 279 CIAT author corrections on CGSpace</li>`
			`</ul>`

Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`<h2 id="2017-03-02">2017-03-02</h2>`

			`<ul>`
Update notes for 2017-03-03 2017-03-04 00:15:47 +01:00			`<li>Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace</li>`
			`<li>CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles</li>`
			`<li>They might come in at the top level in one “CGIAR System” community, or with several communities</li>`
			`<li>I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?</li>`
			`<li>Need to send Peter and Michael some notes about this in a few days</li>`
			`<li>Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI</li>`
Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`<li>Filed an issue on DSpace issue tracker for the <code>filter-media</code> bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: <a href="https://jira.duraspace.org/browse/DS-3516">DS-3516</a></li>`
			`<li>Discovered that the ImageMagic <code>filter-media</code> plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK</li>`
			`<li>Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see <a href="https://cgspace.cgiar.org/handle/10568/51999"><sup>10568</sup>&frasl;<sub>51999</sub></a>):</li>`
			`</ul>`

			`<pre><code>$ identify ~/Desktop/alc_contrastes_desafios.jpg`
			`/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000`
			`</code></pre>`

Update notes for 2017-03-02 2017-03-02 19:00:18 +01:00			`<p></p>`

Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`<ul>`
Update notes for 2017-03-03 2017-03-03 17:40:38 +01:00			`<li>This results in discolored thumbnails when compared to the original PDF, for example sRGB and CMYK:</li>`
Add notes for 2017-03-02 2017-03-02 18:26:39 +01:00			`</ul>`

Update notes for 2017-03-02 2017-03-02 19:00:18 +01:00			`<p><img src="/cgspace-notes/2017/03/thumbnail-srgb.jpg" alt="Thumbnail in sRGB colorspace" /></p>`

Update notes for 2017-03-02 2017-03-02 23:57:37 +01:00			`<p><img src="/cgspace-notes/2017/03/thumbnail-cmyk.jpg" alt="Thumbnial in CMYK colorspace" /></p>`
Add notes for 2017-03-01 2017-03-01 16:10:08 +01:00
Update notes for 2017-03-02 2017-03-03 00:32:54 +01:00			`<ul>`
			`<li>I filed an issue for the color space thing: <a href="https://jira.duraspace.org/browse/DS-3517">DS-3517</a></li>`
			`</ul>`

Update notes for 2017-03-03 2017-03-03 17:40:38 +01:00			`<h2 id="2017-03-03">2017-03-03</h2>`

			`<ul>`
			`<li>I created a patch for DS-3517 and made a pull request against upstream <code>dspace-5_x</code>: <a href="https://github.com/DSpace/DSpace/pull/1669">https://github.com/DSpace/DSpace/pull/1669</a></li>`
			`<li>Looks like <code>-colorspace sRGB</code> alone isn’t enough, we need to use profiles:</li>`
			`</ul>`

Update notes for 2017-03-03 2017-03-04 00:15:47 +01:00			`<pre><code>$ convert alc_contrastes_desafios.pdf\[0\] -profile /opt/brew/Cellar/ghostscript/9.20/share/ghostscript/9.20/iccprofiles/default_cmyk.icc -thumbnail 300x300 -flatten -profile /opt/brew/Cellar/ghostscript/9.20/share/ghostscript/9.20/iccprofiles/default_rgb.icc alc_contrastes_desafios.pdf.jpg`
Update notes for 2017-03-03 2017-03-03 17:40:38 +01:00			`</code></pre>`

			`<ul>`
Update notes for 2017-03-03 2017-03-04 00:15:47 +01:00			`<li>This reads the input file, applies the CMYK profile, applies the RGB profile, then writes the file</li>`
			`<li>Note that you should set the first profile immediately after the input file</li>`
			`<li>Also, it is better to use profiles than setting <code>-colorspace</code></li>`
Update notes for 2017-03-03 2017-03-03 17:40:38 +01:00			`<li>This is a great resource describing the color stuff: <a href="http://www.imagemagick.org/Usage/formats/#profiles">http://www.imagemagick.org/Usage/formats/#profiles</a></li>`
Update notes for 2017-03-03 2017-03-04 00:15:47 +01:00			`<li>Somehow we need to detect the color system being used by the input file and handle each case differently (with profiles)</li>`
Update notes for 2017-03-03 2017-03-03 17:40:38 +01:00			`<li>This is trivial with <code>identify</code> (even by the <a href="http://im4java.sourceforge.net/api/org/im4java/core/IMOps.html#identify">Java ImageMagick API</a>):</li>`
			`</ul>`

			`<pre><code>$ identify -format '%r\n' alc_contrastes_desafios.pdf\[0\]`
			`DirectClass CMYK`
			`$ identify -format '%r\n' Africa\ group\ of\ negotiators.pdf\[0\]`
			`DirectClass sRGB Alpha`
			`</code></pre>`

Add notes for 2017-03-05 2017-03-05 11:39:09 +01:00			`<h2 id="2017-03-05">2017-03-05</h2>`

			`<ul>`
			`<li>Look into helping developers from landportal.info with a query for items related to LAND on the REST API</li>`
			`<li>They want something like the items that are returned by the general “LAND” query in the search interface, but we cannot do that</li>`
			`<li>We can only return specific results for metadata fields, like:</li>`
			`</ul>`

			`<pre><code>$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "LAND REFORM", "language": null}' \| json_pp`
			`</code></pre>`

			`<ul>`
			`<li>But there are hundreds of combinations of fields and values (like <code>dc.subject</code> and all the center subjects), and we can’t use wildcards in REST!</li>`
			`</ul>`

Add notes for 2017-03-01 2017-03-01 16:10:08 +01:00



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