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315 lines
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HTML
315 lines
13 KiB
HTML
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<meta property="og:title" content="August, 2017" />
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<meta property="og:description" content="2017-08-01
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Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours
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I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)
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The good thing is that, according to dspace.log.2017-08-01, they are all using the same Tomcat session
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This means our Tomcat Crawler Session Valve is working
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But many of the bots are browsing dynamic URLs like:
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/handle/10568/3353/discover
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/handle/10568/16510/browse
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The robots.txt only blocks the top-level /discover and /browse URLs… we will need to find a way to forbid them from accessing these!
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Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): https://jira.duraspace.org/browse/DS-2962
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It turns out that we’re already adding the X-Robots-Tag "none" HTTP header, but this only forbids the search engine from indexing the page, not crawling it!
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Also, the bot has to successfully browse the page first so it can receive the HTTP header…
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We might actually have to block these requests with HTTP 403 depending on the user agent
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Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415
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This was due to newline characters in the dc.description.abstract column, which caused OpenRefine to choke when exporting the CSV
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I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
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Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-08/" />
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<meta property="article:published_time" content="2017-08-01T11:51:52+03:00"/>
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<meta property="article:modified_time" content="2017-08-09T17:27:46+03:00"/>
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<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="August, 2017"/>
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<meta name="twitter:description" content="2017-08-01
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Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours
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I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)
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The good thing is that, according to dspace.log.2017-08-01, they are all using the same Tomcat session
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This means our Tomcat Crawler Session Valve is working
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But many of the bots are browsing dynamic URLs like:
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/handle/10568/3353/discover
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/handle/10568/16510/browse
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The robots.txt only blocks the top-level /discover and /browse URLs… we will need to find a way to forbid them from accessing these!
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Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): https://jira.duraspace.org/browse/DS-2962
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It turns out that we’re already adding the X-Robots-Tag "none" HTTP header, but this only forbids the search engine from indexing the page, not crawling it!
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Also, the bot has to successfully browse the page first so it can receive the HTTP header…
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We might actually have to block these requests with HTTP 403 depending on the user agent
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Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415
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This was due to newline characters in the dc.description.abstract column, which caused OpenRefine to choke when exporting the CSV
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I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
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Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
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"/>
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<meta name="generator" content="Hugo 0.26" />
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "August, 2017",
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"url": "https://alanorth.github.io/cgspace-notes/2017-08/",
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"datePublished": "2017-08-01T11:51:52+03:00",
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"author": {
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"name": "Alan Orth"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2017-08/">
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<title>August, 2017 | CGSpace Notes</title>
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<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-j3n8sYdzztDYtVc80KiiuOXoCg5Bjz0zYyLGzDMW8RbfA0u5djbF0GO3bVOPoLyN" crossorigin="anonymous">
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<body>
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<div class="blog-masthead">
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<div class="container">
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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</nav>
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</div>
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</div>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<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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</div>
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</header>
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<div class="container">
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<div class="col-sm-8 blog-main">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-08/">August, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-08-01T11:51:52+03:00">Tue Aug 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-08-01">2017-08-01</h2>
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<ul>
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<li>Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours</li>
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<li>I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)</li>
|
|
<li>The good thing is that, according to <code>dspace.log.2017-08-01</code>, they are all using the same Tomcat session</li>
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<li>This means our Tomcat Crawler Session Valve is working</li>
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<li>But many of the bots are browsing dynamic URLs like:
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<ul>
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<li>/handle/10568/3353/discover</li>
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<li>/handle/10568/16510/browse</li>
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</ul></li>
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<li>The <code>robots.txt</code> only blocks the top-level <code>/discover</code> and <code>/browse</code> URLs… we will need to find a way to forbid them from accessing these!</li>
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<li>Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li>
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<li>It turns out that we’re already adding the <code>X-Robots-Tag "none"</code> HTTP header, but this only forbids the search engine from <em>indexing</em> the page, not crawling it!</li>
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<li>Also, the bot has to successfully browse the page first so it can receive the HTTP header…</li>
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<li>We might actually have to <em>block</em> these requests with HTTP 403 depending on the user agent</li>
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<li>Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415</li>
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<li>This was due to newline characters in the <code>dc.description.abstract</code> column, which caused OpenRefine to choke when exporting the CSV</li>
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<li>I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using <code>g/^$/d</code></li>
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<li>Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet</li>
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</ul>
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<p></p>
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<h2 id="2017-08-02">2017-08-02</h2>
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<ul>
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<li>Magdalena from CCAFS asked if there was a way to get the top ten items published in 2016 (note: not the top items in 2016!)</li>
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<li>I think Atmire’s Content and Usage Analysis module should be able to do this but I will have to look at the configuration and maybe email Atmire if I can’t figure it out</li>
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<li>I had a look at the moduel configuration and couldn’t figure out a way to do this, so I <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-tickets">opened a ticket on the Atmire tracker</a></li>
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<li>Atmire responded about the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=500">missing workflow statistics issue</a> a few weeks ago but I didn’t see it for some reason</li>
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<li>They said they added a publication and saw the workflow stat for the user, so I should try again and let them know</li>
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</ul>
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<h2 id="2017-08-05">2017-08-05</h2>
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<ul>
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<li>Usman from CIFOR emailed to ask about the status of our OAI tests for harvesting their DSpace repository</li>
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<li>I told him that the OAI appears to not be harvesting properly after the first sync, and that the control panel shows an “Internal error” for that collection:</li>
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</ul>
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<p><img src="/cgspace-notes/2017/08/cifor-oai-harvesting.png" alt="CIFOR OAI harvesting" /></p>
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<ul>
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<li>I don’t see anything related in our logs, so I asked him to check for our server’s IP in their logs</li>
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<li>Also, in the mean time I stopped the harvesting process, reset the status, and restarted the process via the Admin control panel (note: I didn’t reset the collection, just the harvester status!)</li>
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</ul>
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<h2 id="2017-08-07">2017-08-07</h2>
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<ul>
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<li>Apply Abenet’s corrections for the CGIAR Library’s Consortium subcommunity (697 records)</li>
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<li>I had to fix a few small things, like moving the <code>dc.title</code> column away from the beginning of the row, delete blank spaces in the abstract in vim using <code>:g/^$/d</code>, add the <code>dc.subject[en_US]</code> column back, as she had deleted it and DSpace didn’t detect the changes made there (we needed to blank the values instead)</li>
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</ul>
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<h2 id="2017-08-08">2017-08-08</h2>
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<ul>
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<li>Apply Abenet’s corrections for the CGIAR Library’s historic archive subcommunity (2415 records)</li>
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<li>I had to add the <code>dc.subject[en_US]</code> column back with blank values so that DSpace could detect the changes</li>
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<li>I applied the changes in 500 item batches</li>
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</ul>
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<h2 id="2017-08-09">2017-08-09</h2>
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<ul>
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<li>Run system updates on DSpace Test and reboot server</li>
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<li>Help ICARDA upgrade their MELSpace to DSpace 5.7 using the <a href="https://github.com/alanorth/docker-dspace">docker-dspace</a> container
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<ul>
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<li>We had to import the PostgreSQL dump to the PostgreSQL container using: <code>pg_restore -U postgres -d dspace blah.dump</code></li>
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<li>Otherwise, when using <code>-O</code> it messes up the permissions on the schema and DSpace can’t read it</li>
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</ul></li>
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</ul>
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<h2 id="2017-08-10">2017-08-10</h2>
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<ul>
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<li>Apply last updates to the CGIAR Library’s Fund community (812 items)</li>
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<li>Had to do some quality checks and column renames before importing, as either Sisay or Abenet renamed a few columns and the metadata importer wanted to remove/add new metadata for title, abstract, etc.</li>
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<li>Also I applied the HTML entities unescape transform on the abstract column in Open Refine</li>
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<li>I need to get an author list from the database for only the CGIAR Library community to send to Peter</li>
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<li>Meeting with Peter and CGSpace team
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<ul>
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<li>Alan to follow up with ICARDA about depositing in CGSpace, we want ICARD and Drylands legacy content but not duplicates</li>
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<li>Alan to follow up on dc.rights, where are we?</li>
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<li>Alan to follow up with Atmire about a dedicated field for ORCIDs, based on the discussion in the <a href="https://wiki.duraspace.org/display/cmtygp/DCAT+Meeting+June+2017">June, 2017 DCAT meeting</a></li>
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<li>Alan to ask about how to query external services like AGROVOC in the DSpace submission form</li>
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</ul></li>
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</ul>
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 offset-sm-1 blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2017-08/">August, 2017</a></li>
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<li><a href="/cgspace-notes/2017-07/">July, 2017</a></li>
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<li><a href="/cgspace-notes/2017-06/">June, 2017</a></li>
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<li><a href="/cgspace-notes/2017-05/">May, 2017</a></li>
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<li><a href="/cgspace-notes/2017-04/">April, 2017</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p>
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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