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Export CGSpace to check for missing Initiative collection mappings
Start a harvest on AReS
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Export CGSpace to check for missing Initiative collection mappings
Start a harvest on AReS
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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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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2023-09/">September, 2023</a></h2>
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<time datetime="2023-09-02T17:29:36+03:00">Sat Sep 02, 2023</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2023-09-02">2023-09-02</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-09-03">2023-09-03</h2>
<ul>
<li>I figured out how to use Altmetric and Dimensions badges in the DSpace Angular frontend
<ul>
<li>It still feels hacky, but using <a href="https://stackoverflow.com/questions/41936631/how-to-trigger-the-function-after-dom-markup-is-loaded-in-angular-style-applicat">AfterViewInit</a>, and importing the Altmetric <code>embed.js</code> in the component works</li>
<li>The style on mobile also needs work&hellip;</li>
</ul>
</li>
</ul>
<h2 id="2023-09-06">2023-09-06</h2>
<ul>
<li>Discussion with Marie about finalizing the output types list on GitHub
<ul>
<li>I did some review and cleanup in preparation for publishing the new list</li>
</ul>
</li>
</ul>
<h2 id="2023-09-07">2023-09-07</h2>
<ul>
<li>Export CGSpace to start doing a review of the metadata</li>
<li>First I will start by extracting all items with DOIs, along with some fields I can compare against Crossref:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvgrep -c <span style="color:#e6db74">&#39;cg.identifier.doi[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;doi.org&#39;</span> ~/Downloads/2023-09-07-cgspace.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c &#39;id,dc.title[en_US],dcterms.issued[en_US],dcterms.available[en_US],cg.issn[en_US],cg.isbn[en_US],cg.volume[en_US],cg.issue[en_US],cg.number[en_US],dcterms.extent[en_US],cg.identifier.doi[en_US],cg.reviewStatus[en_US],cg.isijournal[en_US],dcterms.license[en_US],dcterms.accessRights[en_US],dcterms.type[en_US],dc.identifier.uri[en_US]&#39; \
</span></span><span style="display:flex;"><span> &gt; /tmp/2023-09-07-cgspace-dois.csv
</span></span><span style="display:flex;"><span>$ csvgrep -c <span style="color:#e6db74">&#39;cg.identifier.doi[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;doi.org&#39;</span> ~/Downloads/2023-09-07-cgspace.csv | csvcut -c <span style="color:#e6db74">&#39;cg.identifier.doi[en_US]&#39;</span> | sed 1d &gt; /tmp/2023-09-07-cgspace-dois.txt
</span></span></code></pre></div><ul>
<li>Then I resolved the DOIs from Crossref:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./ilri/crossref_doi_lookup.py -i /tmp/2023-09-07-cgspace-dois.txt -o /tmp/2023-09-07-cgspace-dois-results.csv -e a.orth@cgiar.org
</span></span></code></pre></div><ul>
<li>A user emailed to ask about uploading a 180MB PDF to CGSpace
<ul>
<li>I used GhostScript to try reducing it using the <code>screen</code>, <code>ebook</code> and <code>prepress</code> presets:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>primer-screen.pdf Primer<span style="color:#ae81ff">\ \(</span>digital<span style="color:#ae81ff">\)</span>_Climate-<span style="color:#ae81ff">\ </span>smart<span style="color:#ae81ff">\ </span>and<span style="color:#ae81ff">\ </span>regenerative<span style="color:#ae81ff">\ </span>agriculture<span style="color:#ae81ff">\ </span>in<span style="color:#ae81ff">\ </span>climate<span style="color:#ae81ff">\ </span>change<span style="color:#ae81ff">\ </span>adaptation.pdf
</span></span><span style="display:flex;"><span>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/ebook -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>primer-ebook.pdf Primer<span style="color:#ae81ff">\ \(</span>digital<span style="color:#ae81ff">\)</span>_Climate-<span style="color:#ae81ff">\ </span>smart<span style="color:#ae81ff">\ </span>and<span style="color:#ae81ff">\ </span>regenerative<span style="color:#ae81ff">\ </span>agriculture<span style="color:#ae81ff">\ </span>in<span style="color:#ae81ff">\ </span>climate<span style="color:#ae81ff">\ </span>change<span style="color:#ae81ff">\ </span>adaptation.pdf
</span></span><span style="display:flex;"><span>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/prepress -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>primer-prepress.pdf Primer<span style="color:#ae81ff">\ \(</span>digital<span style="color:#ae81ff">\)</span>_Climate-<span style="color:#ae81ff">\ </span>smart<span style="color:#ae81ff">\ </span>and<span style="color:#ae81ff">\ </span>regenerative<span style="color:#ae81ff">\ </span>agriculture<span style="color:#ae81ff">\ </span>in<span style="color:#ae81ff">\ </span>climate<span style="color:#ae81ff">\ </span>change<span style="color:#ae81ff">\ </span>adaptation.pdf
</span></span></code></pre></div><ul>
<li>The <code>prepress</code> one is 300DPI and looks visually identical to the original, so I proposed that we use that one</li>
</ul>
<h2 id="2023-09-08">2023-09-08</h2>
<ul>
<li>I did a review of the metadata for our items with DOIs, comparing with data from Crossref
<ul>
<li>I spot checked a handful of issue / online dates and licenses, and saw that Crossref&rsquo;s dates are always more accurate than ours when they differ</li>
<li>I also filled in some missing volumes, issues, ISSNs, and extents</li>
<li>This results in 14,000 changes to existing items, which will take several days to import unfortunately</li>
<li>After eight hours the first file is only about 2/3 finished&hellip; sigh</li>
</ul>
</li>
<li>Meet with Peter to discuss changes to the DSpace 7 test
<ul>
<li>Minor updates to submission forms and some new ideas for the home page and item page</li>
</ul>
</li>
<li>I figured out how to use a themed home page component and add a cards UI to our CGSpace theme</li>
</ul>
<h2 id="2023-09-09">2023-09-09</h2>
<ul>
<li>I can&rsquo;t believe that almost 18 hours later the first CSV import with 5,000 changes is not done&hellip;</li>
<li>Run all system updates on CGSpace and reboot it, as it had been two months since the last time</li>
</ul>
<h2 id="2023-09-10">2023-09-10</h2>
<ul>
<li>Minor work on the DSpace 7 home page</li>
</ul>
<h2 id="2023-09-11">2023-09-11</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-09-12">2023-09-12</h2>
<ul>
<li>Minor work on DSpace 7 home page</li>
<li>Minor work on CG Core types
<ul>
<li>I published a new HTML version of the updated IPtypes and archived the current version as v2.0.0 so we can still reference it</li>
</ul>
</li>
</ul>
<h2 id="2023-09-13">2023-09-13</h2>
<ul>
<li>Stefano reminded me about the updated OAI MODS mappings on CGSpace so I re-applied them on DSpace Test and updated the OAI index so he could confirm
<ul>
<li>Now I&rsquo;m ready to put it on CGSpace if he confirms</li>
</ul>
</li>
<li>I created a basic theme for CIP on DSpace 7
<ul>
<li>While doing that I noticed that a bunch of CIP bitstreams didn&rsquo;t have the latest 500px thumbnails so I re-ran filter-media on a handful of their collections</li>
</ul>
</li>
<li>I had two occurrences of an OOM kill of the Tomcat 9 java process on DSpace 7 test tonight
<ul>
<li>Once while doing a Discovery index, the other while doing filter media</li>
</ul>
</li>
</ul>
<h2 id="2023-09-15">2023-09-15</h2>
<ul>
<li>Discuss issues with the Altmetric API with the Altmetric support team
<ul>
<li>Apparently we can use a different API, the <a href="https://www.altmetric.com/explorer/documentation/api">Explorer API</a>, since we already have access to the Explorer dashboard</li>
</ul>
</li>
<li>I reduced the Solr heap size on DSpace 7 from 3GB to 2GB
<ul>
<li>Apparentlty I already did this from 4GB to 3GB a few months ago</li>
<li>The Solr admin interface was showing Solr taking ~1GB of RAM so I think this should be safe</li>
</ul>
</li>
<li>Mark on DSpace Slack said he uses PM2&rsquo;s <code>--max-memory-restart</code> so the processes restart when they hit the limit
<ul>
<li>Also, he said he had to reduce <code>cache:serverSide:botCache:max</code> from 1000 to 500 to cache less SSR pages in memory</li>
</ul>
</li>
<li>I decided to try deploying DSpace 7 Test on a Hetzner server with 64GB RAM, 6 CPUs, and 2x512GB NVMe SSD</li>
</ul>
<h2 id="2023-09-16">2023-09-16</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
<li>Configure the privacy policy page on DSpace 7 using a themed component with the text from our DSpace 6 site</li>
<li>I realized that for all my custom Angular components I should be using <code>routerLink</code> instead of <code>href</code> when I am constructing links
<ul>
<li>The <code>routerLink</code> routes within the single page application and saves state, while the <code>href</code> reloads the page</li>
<li>Using the <code>routerLink</code> way is faster and results in less flashing and jumping in the page when navigating</li>
<li>See: <a href="https://stackoverflow.com/a/61588147">https://stackoverflow.com/a/61588147</a></li>
</ul>
</li>
</ul>
<h2 id="2023-09-17">2023-09-17</h2>
<ul>
<li>I added an About page to DSpace 7 Test using similar logic to the privacy page</li>
</ul>
<h2 id="2023-09-18">2023-09-18</h2>
<ul>
<li>I filed a GitHub issue for being unable to navigate dropdown lists using the keyboard on the dspace-angular submission form: <a href="https://github.com/DSpace/dspace-angular/issues/2500">https://github.com/DSpace/dspace-angular/issues/2500</a></li>
<li>I filed a GitHub issue for the search filters capitalizing metadata values: <a href="https://github.com/DSpace/dspace-angular/issues/2501">https://github.com/DSpace/dspace-angular/issues/2501</a></li>
</ul>
<h2 id="2023-09-19">2023-09-19</h2>
<ul>
<li>Complete migration of DSpace 7 Test from Linode to Hetzner</li>
<li>Export some years of Solr stats from CGSpace to import on the new DSpace 7 Test:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/statistics-2020-2022.json -f <span style="color:#e6db74">&#39;time:[2020-01-01T00\:00\:00Z TO 2022-12-31T23\:59\:59Z]&#39;</span> -k uid -S actingGroupId,actingGroupParentId,actorMemberGroupId,author_mtdt,author_mtdt_search,bitstreamCount,bitstreamId,complete_query,complete_query_search,containerBitstream,containerCollection,containerCommunity,containerItem,core_update_run_nb,countryCode_ngram,countryCode_search,cua_version,dateYear,dateYearMonth,file_id,filterquery,first_name,geoipcountrycode,geoIpCountryCode,group_id,group_map,group_name,ip_ngram,ip_search,isArchived,isInternal,iso_mtdt,iso_mtdt_search,isWithdrawn,last_name,name,ngram_query_search,ngram_simplequery_search,orphaned,parent_count,p_communities_id,p_communities_map,p_communities_name,p_group_id,p_group_map,p_group_name,range,rangeDescription,rangeDescription_ngram,rangeDescription_search,range_ngram,range_search,referrer_ngram,referrer_search,simple_query,simple_query_search,solr_update_time_stamp,storage_nb_of_bitstreams,storage_size,storage_statistics_type,subject_mtdt,subject_mtdt_search,text,userAgent_ngram,userAgent_search,version_id,workflowItemId
</span></span></code></pre></div><ul>
<li>Ben sent me an export of ILRI presentations from Slideshare and asked if we could see if any are missing on CGSpace
<ul>
<li>First I exported CGSpace and extracted the <code>cg.identifier.url</code> column so I could normalize all Slideshare URLs to use &ldquo;<a href="https://www.slideshare.net">https://www.slideshare.net</a>&rdquo; instead of localized variants (es.slideshare.net, fr.slideshare.net, etc) as well as non-https links and links with query params and slashes at the end</li>
<li>This was about 250 URLs</li>
</ul>
</li>
<li>I extracted the URL field from both our list and the Slideshare list and then used <a href="https://unix.stackexchange.com/questions/274548/join-two-files-each-with-two-columns-including-non-matching-lines">GNU <code>join</code> to print non-matched lines</a>:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ join -t, -v <span style="color:#ae81ff">2</span> -11 -21 -o auto /tmp/cgspace-ilri-slideshare-sorted-only-urls-sorted.csv /tmp/ilri-slideshare-sorted-sorted.csv | wc -l
</span></span><span style="display:flex;"><span>542
</span></span></code></pre></div><ul>
<li>Important to note that you must use GNU <code>sort</code> on the fiels first, as I had tried sorting in vim and it didn&rsquo;t satisfy <code>join</code></li>
<li>So it seems there are 542 Slideshare presentations we are missing</li>
</ul>
<h2 id="2023-09-20">2023-09-20</h2>
<ul>
<li>Regarding the incorrect city in Solr statistics, I see we have 1,600,000 of them
<ul>
<li>Before filing a GitHub issue, I want to check if they maybe come from an Atmire module, as I see them clustered around two particular CUA versions:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-json" data-lang="json"><span style="display:flex;"><span>{
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</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;status&#34;</span>: <span style="color:#ae81ff">0</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;QTime&#34;</span>: <span style="color:#ae81ff">2760</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;params&#34;</span>: {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;q&#34;</span>: <span style="color:#e6db74">&#34;city:com.maxmind.geoip2.record.City*&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;facet.field&#34;</span>: <span style="color:#e6db74">&#34;cua_version&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;indent&#34;</span>: <span style="color:#e6db74">&#34;true&#34;</span>,
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</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;facet&#34;</span>: <span style="color:#e6db74">&#34;true&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;_&#34;</span>: <span style="color:#e6db74">&#34;1695192301927&#34;</span>
</span></span><span style="display:flex;"><span> }
</span></span><span style="display:flex;"><span> },
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;response&#34;</span>: {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;numFound&#34;</span>: <span style="color:#ae81ff">1661863</span>,
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</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;docs&#34;</span>: []
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</span></span><span style="display:flex;"><span> <span style="color:#e6db74">&#34;6.x-4.1.10-ilri-RC7&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#ae81ff">1112186</span>,
</span></span><span style="display:flex;"><span> <span style="color:#e6db74">&#34;6.x-4.1.10-ilri-RC5&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#ae81ff">451180</span>,
</span></span><span style="display:flex;"><span> <span style="color:#e6db74">&#34;6.x-4.1.10-ilri-RC9&#34;</span>,
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</span></span><span style="display:flex;"><span> ]
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</span></span></code></pre></div><ul>
<li>I migrated AReS from Linode to Hetzner</li>
<li>I asked on Slack and someone told me that we need to edit <code>src/app/menu.resolver.ts</code> to add new drop down menus to the top navbar
<ul>
<li>It works, though is unfortunate that we can&rsquo;t do it in a theme</li>
</ul>
</li>
</ul>
<h2 id="2023-09-21">2023-09-21</h2>
<ul>
<li>More minor work on DSpace 7 home page and menus</li>
<li>Meeting to discuss types and DSpace 7 migration plans</li>
<li>Create a DSpace 7 theme for IITA</li>
</ul>
<h2 id="2023-09-22">2023-09-22</h2>
<ul>
<li>Create a DSpace 7 theme for IWMI</li>
<li>I had some issues with pm2 on the new DSpace 7 Test
<ul>
<li>It seems to be due to mixing systemd starting versus manually starting / stopping&hellip;</li>
<li>After reading the discussion in <a href="https://github.com/Unitech/pm2/issues/2914">this pm2 issue</a> I realize that we probably need to use <code>--no-daemon</code> to have systemd fully manage the processes without pm2 trying to save state</li>
</ul>
</li>
</ul>
<h2 id="2023-09-23">2023-09-23</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-09-25">2023-09-25</h2>
<ul>
<li>CGSpace metadata and community / collection cleanup</li>
<li>Review some patches on DSpace Angular</li>
<li>Create a basic Alliance theme for DSpace 7</li>
</ul>
<h2 id="2023-09-27">2023-09-27</h2>
<ul>
<li>I realized that we can get controlled vocabularies from DSpace 7&rsquo;s REST API, for both value-pairs and hierarchical controlled vocabularies, ie:</li>
</ul>
<p><a href="https://dspace7test.ilri.org/server/api/submission/vocabularies/common_iso_languages/entries">https://dspace7test.ilri.org/server/api/submission/vocabularies/common_iso_languages/entries</a></p>
<h2 id="2023-09-29">2023-09-29</h2>
<ul>
<li>Meeting with Aditi and others to discuss plan for using CGSpace to do a systematic review of CGIAR research on climate change</li>
<li>I cleaned up metadata for a hundred or so items, and realized we will need to do more to make sure abstracts and open access status are correct since there will be a laser focus on the metadata</li>
</ul>
<h2 id="2023-09-30">2023-09-30</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Still working on checking Unpaywall for access rights and licenses for our DOIs</li>
<li>Regarding Unpaywall&rsquo;s &ldquo;evidence&rdquo; metadata about whether an item is open access or not, after looking at dozens of items manually:
<ul>
<li>evidence: &ldquo;oa journal (via doaj)&rdquo; &lt;&mdash;- yes</li>
<li>evidence: &ldquo;open (via free article)&rdquo; &lt;&mdash;- hmmm, not always correct</li>
<li>evidence: &ldquo;open (via page says license)&rdquo; &lt;&mdash; noooo, can&rsquo;t rely on that</li>
<li>evidence: &ldquo;open (via page says Open Access)&rdquo; &lt;&mdash;- yes&hellip;?</li>
<li>evidence: &ldquo;open (via free pdf)&rdquo; &lt;&mdash;- hmmm, not always correct</li>
<li>evidence: &ldquo;oa journal (via publisher name)&rdquo; &lt;&mdash;- noooo</li>
</ul>
</li>
<li>I updated access status for about four hundred more items based on this, and licenses for a dozen or so</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2023-10/">October, 2023</a></li>
<li><a href="/cgspace-notes/2023-09/">September, 2023</a></li>
<li><a href="/cgspace-notes/2023-08/">August, 2023</a></li>
<li><a href="/cgspace-notes/2023-07/">July, 2023</a></li>
<li><a href="/cgspace-notes/2023-06/">June, 2023</a></li>
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<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>
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