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<meta property="og:description" content="2017-03-01
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Run the 279 CIAT author corrections on CGSpace
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2017-03-02
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Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
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CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
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They might come in at the top level in one “CGIAR System” community, or with several communities
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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?
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Need to send Peter and Michael some notes about this in a few days
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Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
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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
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Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
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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 10568/51999):
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$ identify ~/Desktop/alc_contrastes_desafios.jpg
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/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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<meta name="twitter:title" content="March, 2017"/>
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<meta name="twitter:description" content="2017-03-01
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Run the 279 CIAT author corrections on CGSpace
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2017-03-02
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Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
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CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
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They might come in at the top level in one “CGIAR System” community, or with several communities
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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?
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Need to send Peter and Michael some notes about this in a few days
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Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
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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
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Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
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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 10568/51999):
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$ identify ~/Desktop/alc_contrastes_desafios.jpg
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/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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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">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" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-03/">March, 2017</a></h2>
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<time datetime="2017-03-01T17:08:52+02:00">Wed Mar 01, 2017</time>
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in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
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</header>
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<h2 id="2017-03-01">2017-03-01</h2>
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<ul>
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<li>Run the 279 CIAT author corrections on CGSpace</li>
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</ul>
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<h2 id="2017-03-02">2017-03-02</h2>
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<ul>
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<li>Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace</li>
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<li>CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles</li>
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<li>They might come in at the top level in one “CGIAR System” community, or with several communities</li>
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<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>
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<li>Need to send Peter and Michael some notes about this in a few days</li>
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<li>Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI</li>
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<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>
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<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>
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<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">10568/51999</a>):</li>
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</ul>
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<pre tabindex="0"><code>$ identify ~/Desktop/alc_contrastes_desafios.jpg
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/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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</code></pre><ul>
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<li>This results in discolored thumbnails when compared to the original PDF, for example sRGB and CMYK:</li>
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</ul>
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<p><img src="/cgspace-notes/2017/03/thumbnail-srgb.jpg" alt="Thumbnail in sRGB colorspace"></p>
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<p><img src="/cgspace-notes/2017/03/thumbnail-cmyk.jpg" alt="Thumbnial in CMYK colorspace"></p>
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<ul>
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<li>I filed an issue for the color space thing: <a href="https://jira.duraspace.org/browse/DS-3517">DS-3517</a></li>
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</ul>
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<h2 id="2017-03-03">2017-03-03</h2>
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<ul>
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<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>
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<li>Looks like <code>-colorspace sRGB</code> alone isn’t enough, we need to use profiles:</li>
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</ul>
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<pre tabindex="0"><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
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</code></pre><ul>
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<li>This reads the input file, applies the CMYK profile, applies the RGB profile, then writes the file</li>
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<li>Note that you should set the first profile immediately after the input file</li>
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<li>Also, it is better to use profiles than setting <code>-colorspace</code></li>
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<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>
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<li>Somehow we need to detect the color system being used by the input file and handle each case differently (with profiles)</li>
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<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>
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</ul>
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<pre tabindex="0"><code>$ identify -format '%r\n' alc_contrastes_desafios.pdf\[0\]
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DirectClass CMYK
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$ identify -format '%r\n' Africa\ group\ of\ negotiators.pdf\[0\]
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DirectClass sRGB Alpha
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</code></pre><h2 id="2017-03-04">2017-03-04</h2>
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<ul>
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<li>Spent more time looking at the ImageMagick CMYK issue</li>
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<li>The <code>default_cmyk.icc</code> and <code>default_rgb.icc</code> files are both part of the Ghostscript GPL distribution, but according to DSpace’s <code>LICENSES_THIRD_PARTY</code> file, DSpace doesn’t allow distribution of dependencies that are licensed solely under the GPL</li>
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<li>So this issue is kinda pointless now, as the ICC profiles are absolutely necessary to make a meaningful CMYK→sRGB conversion</li>
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</ul>
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<h2 id="2017-03-05">2017-03-05</h2>
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<ul>
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<li>Look into helping developers from landportal.info with a query for items related to LAND on the REST API</li>
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<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>
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<li>We can only return specific results for metadata fields, like:</li>
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</ul>
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<pre tabindex="0"><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
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</code></pre><ul>
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<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>
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<li>Reading about enabling multiple handle prefixes in DSpace</li>
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<li>There is a mailing list thread from 2011 about it: <a href="http://dspace.2283337.n4.nabble.com/Multiple-handle-prefixes-merged-DSpace-instances-td3427192.html">http://dspace.2283337.n4.nabble.com/Multiple-handle-prefixes-merged-DSpace-instances-td3427192.html</a></li>
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<li>And a comment from Atmire’s Bram about it on the DSpace wiki: <a href="https://wiki.lyrasis.org/display/DSDOC5x/Installing+DSpace?focusedCommentId=78163296#comment-78163296">https://wiki.lyrasis.org/display/DSDOC5x/Installing+DSpace?focusedCommentId=78163296#comment-78163296</a></li>
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<li>Bram mentions an undocumented configuration option <code>handle.plugin.checknameauthority</code>, but I noticed another one in <code>dspace.cfg</code>:</li>
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</ul>
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<pre tabindex="0"><code># List any additional prefixes that need to be managed by this handle server
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# (as for examle handle prefix coming from old dspace repository merged in
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# that repository)
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# handle.additional.prefixes = prefix1[, prefix2]
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</code></pre><ul>
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<li>Because of this I noticed that our Handle server’s <code>config.dct</code> was potentially misconfigured!</li>
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<li>We had some default values still present:</li>
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</ul>
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<pre tabindex="0"><code>"300:0.NA/YOUR_NAMING_AUTHORITY"
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</code></pre><ul>
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<li>I’ve changed them to the following and restarted the handle server:</li>
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</ul>
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<pre tabindex="0"><code>"300:0.NA/10568"
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</code></pre><ul>
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<li>In looking at all the configs I just noticed that we are not providing a DOI in the Google-specific metadata crosswalk</li>
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<li>From <code>dspace/config/crosswalks/google-metadata.properties</code>:</li>
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</ul>
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<pre tabindex="0"><code>google.citation_doi = cg.identifier.doi
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</code></pre><ul>
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<li>This works, and makes DSpace output the following metadata on the item view page:</li>
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</ul>
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<pre tabindex="0"><code><meta content="https://dx.doi.org/10.1186/s13059-017-1153-y" name="citation_doi">
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</code></pre><ul>
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<li>Submitted and merged pull request for this: <a href="https://github.com/ilri/DSpace/pull/305">https://github.com/ilri/DSpace/pull/305</a></li>
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<li>Submit pull request to set the author separator for XMLUI item lists to a semicolon instead of “,”: <a href="https://github.com/ilri/DSpace/pull/306">https://github.com/ilri/DSpace/pull/306</a></li>
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<li>I want to show it briefly to Abenet and Peter to get feedback</li>
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</ul>
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<h2 id="2017-03-06">2017-03-06</h2>
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<ul>
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<li>Someone on the mailing list said that <code>handle.plugin.checknameauthority</code> should be false if we’re using multiple handle prefixes</li>
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</ul>
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<h2 id="2017-03-07">2017-03-07</h2>
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<ul>
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<li>I set up a top-level community as a test for the CGIAR Library and imported one item with the the 10947 handle prefix</li>
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<li>When testing the Handle resolver locally it shows the item to be on the local repository</li>
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<li>So this seems to work, with the following caveats:
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<ul>
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<li>New items will have the default handle</li>
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<li>Communities and collections will have the default handle</li>
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<li>Only items imported manually can have the other handles</li>
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</ul>
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</li>
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<li>I need to talk to Michael and Peter to share the news, and discuss the structure of their community(s) and try some actual test data</li>
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<li>We’ll need to do some data cleaning to make sure they are using the same fields we are, like <code>dc.type</code> and <code>cg.identifier.status</code></li>
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<li>Another thing is that the import process creates new <code>dc.date.accessioned</code> and <code>dc.date.available</code> fields, so we end up with duplicates (is it important to preserve the originals for these?)</li>
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<li>Report DS-3520 issue to Atmire</li>
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</ul>
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<h2 id="2017-03-08">2017-03-08</h2>
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<ul>
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<li>Merge the author separator changes to <code>5_x-prod</code>, as everyone has responded positively about it, and it’s the default in Mirage2 afterall!</li>
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<li>Cherry pick the <code>commons-collections</code> patch from DSpace’s <code>dspace-5_x</code> branch to address DS-3520: <a href="https://jira.duraspace.org/browse/DS-3520">https://jira.duraspace.org/browse/DS-3520</a></li>
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</ul>
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<h2 id="2017-03-09">2017-03-09</h2>
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<ul>
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<li>Export list of sponsors so Peter can clean it up:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'description' and qualifier = 'sponsorship') group by text_value order by count desc) to /tmp/sponsorship.csv with csv;
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COPY 285
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</code></pre><h2 id="2017-03-12">2017-03-12</h2>
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<ul>
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<li>Test the sponsorship fixes and deletes from Peter:</li>
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</ul>
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i Investors-Fix-51.csv -f dc.description.sponsorship -t Action -m 29 -d dspace -u dspace -p fuuuu
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$ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.sponsorship -m 29 -d dspace -u dspace -p fuuu
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</code></pre><ul>
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<li>Generate a new list of unique sponsors so we can update the controlled vocabulary:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# \copy (select distinct text_value from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'description' and qualifier = 'sponsorship')) to /tmp/sponsorship.csv with csv;
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</code></pre><ul>
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<li>Pull request for controlled vocabulary if Peter approves: <a href="https://github.com/ilri/DSpace/pull/308">https://github.com/ilri/DSpace/pull/308</a></li>
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<li>Review Sisay’s roots, tubers, and bananas (RTB) theme, which still needs some fixes to work properly: <a href="https://github.com/ilri/DSpace/pull/307">https://github.com/ilri/DSpace/pull/307</a></li>
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<li>Created an issue to track the progress on the Livestock CRP theme: <a href="https://github.com/ilri/DSpace/issues/309">https://github.com/ilri/DSpace/issues/309</a></li>
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<li>Created a basic theme for the Livestock CRP community</li>
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</ul>
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<p><img src="/cgspace-notes/2017/03/livestock-theme.png" alt="Livestock CRP theme"></p>
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<h2 id="2017-03-15">2017-03-15</h2>
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<ul>
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<li>Merge pull request for controlled vocabulary updates for sponsor: <a href="https://github.com/ilri/DSpace/pull/308">https://github.com/ilri/DSpace/pull/308</a></li>
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<li>Merge pull request for Livestock CRP theme: <a href="https://github.com/ilri/DSpace/issues/309">https://github.com/ilri/DSpace/issues/309</a></li>
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<li>Create pull request for PABRA subjects (waiting for confirmation from Abenet before merging): <a href="https://github.com/ilri/DSpace/pull/310">https://github.com/ilri/DSpace/pull/310</a></li>
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<li>Create pull request for CCAFS Phase II migrations (waiting for confirmation from CCAFS people): <a href="https://github.com/ilri/DSpace/pull/311">https://github.com/ilri/DSpace/pull/311</a></li>
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<li>I also need to ask if either of these new fields need to be added to Discovery facets, search, and Atmire modules</li>
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<li>Run all system updates on DSpace Test and re-deploy CGSpace</li>
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</ul>
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<h2 id="2017-03-16">2017-03-16</h2>
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<ul>
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<li>Merge pull request for PABRA subjects: <a href="https://github.com/ilri/DSpace/pull/310">https://github.com/ilri/DSpace/pull/310</a></li>
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<li>Abenet and Peter say we can add them to Discovery, Atmire modules, etc, but I might not have time to do it now</li>
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<li>Help Sisay with RTB theme again</li>
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<li>Remove ICARDA subject from Discovery sidebar facets: <a href="https://github.com/ilri/DSpace/pull/312">https://github.com/ilri/DSpace/pull/312</a></li>
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<li>Remove ICARDA subject from Browse and item submission form: <a href="https://github.com/ilri/DSpace/pull/313">https://github.com/ilri/DSpace/pull/313</a></li>
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<li>Merge the CCAFS Phase II changes but hold off on doing the flagship metadata updates until Macaroni Bros gets their importer updated</li>
|
||
<li>Deploy latest changes and investor fixes/deletions on CGSpace</li>
|
||
<li>Run system updates on CGSpace and reboot server</li>
|
||
</ul>
|
||
<h2 id="2017-03-20">2017-03-20</h2>
|
||
<ul>
|
||
<li>Create basic XMLUI theme for PABRA community: <a href="https://github.com/ilri/DSpace/pull/315">https://github.com/ilri/DSpace/pull/315</a></li>
|
||
</ul>
|
||
<h2 id="2017-03-24">2017-03-24</h2>
|
||
<ul>
|
||
<li>Still helping Sisay try to figure out how to create a theme for the RTB community</li>
|
||
</ul>
|
||
<h2 id="2017-03-28">2017-03-28</h2>
|
||
<ul>
|
||
<li>CCAFS said they are ready for the flagship updates for Phase II to be run (<code>cg.subject.ccafs</code>), so I ran them on CGSpace:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i ccafs-flagships-feb7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu
|
||
</code></pre><ul>
|
||
<li>We’ve been waiting since February to run these</li>
|
||
<li>Also, I generated a list of all CCAFS flagships because there are a dozen or so more than there should be:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=210 group by text_value order by count desc) to /tmp/ccafs.csv with csv;
|
||
</code></pre><ul>
|
||
<li>I sent a list to CCAFS people so they can tell me if some should be deleted or moved, etc</li>
|
||
<li>Test, squash, and merge Sisay’s RTB theme into <code>5_x-prod</code>: <a href="https://github.com/ilri/DSpace/pull/316">https://github.com/ilri/DSpace/pull/316</a></li>
|
||
</ul>
|
||
<h2 id="2017-03-29">2017-03-29</h2>
|
||
<ul>
|
||
<li>Dump a list of fields in the DC and CG schemas to compare with CG Core:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# select case when metadata_schema_id=1 then 'dc' else 'cg' end as schema, element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id in (1, 2);
|
||
</code></pre><ul>
|
||
<li>Ooh, a better one!</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# select coalesce(case when metadata_schema_id=1 then 'dc.' else 'cg.' end) || concat_ws('.', element, qualifier) as field, scope_note from metadatafieldregistry where metadata_schema_id in (1, 2);
|
||
</code></pre><h2 id="2017-03-30">2017-03-30</h2>
|
||
<ul>
|
||
<li>Adjust the Linode CPU usage alerts for the CGSpace server from 150% to 200%, as generally the nightly Solr indexing causes a usage around 150–190%, so this should make the alerts less regular</li>
|
||
<li>Adjust the threshold for DSpace Test from 90 to 100%</li>
|
||
</ul>
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
|
||
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||
|
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<aside class="col-sm-3 ml-auto blog-sidebar">
|
||
|
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|
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<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-02/">February, 2024</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<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>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
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|
||
|
||
|
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