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<meta property="og:description" content="2021-04-01
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I wrote a script to query Sherpa’s API for our ISSNs: sherpa-issn-lookup.py
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I’m curious to see how the results compare with the results from Crossref yesterday
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AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
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I simply took everything down with docker-compose and then back up, and then it was OK
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Perhaps one of the containers crashed, I should have looked closer but I was in a hurry
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<meta name="twitter:description" content="2021-04-01
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I wrote a script to query Sherpa’s API for our ISSNs: sherpa-issn-lookup.py
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I’m curious to see how the results compare with the results from Crossref yesterday
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AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
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I simply took everything down with docker-compose and then back up, and then it was OK
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Perhaps one of the containers crashed, I should have looked closer but I was in a hurry
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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/2021-04/">April, 2021</a></h2>
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<time datetime="2021-04-01T09:50:54+03:00">Thu Apr 01, 2021</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2021-04-01">2021-04-01</h2>
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<ul>
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<li>I wrote a script to query Sherpa’s API for our ISSNs: <code>sherpa-issn-lookup.py</code>
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<ul>
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<li>I’m curious to see how the results compare with the results from Crossref yesterday</li>
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</ul>
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</li>
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<li>AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
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<ul>
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<li>I simply took everything down with docker-compose and then back up, and then it was OK</li>
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<li>Perhaps one of the containers crashed, I should have looked closer but I was in a hurry</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-04-03">2021-04-03</h2>
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<ul>
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<li>Biruk from ICT contacted me to say that some CGSpace users still can’t log in
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<ul>
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<li>I guess the CGSpace LDAP bind account is really still locked after last week’s reset</li>
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<li>He fixed the account and then I was finally able to bind and query:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "cgspace-account" -W "(sAMAccountName=otheraccounttoquery)"
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</code></pre><h2 id="2021-04-04">2021-04-04</h2>
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<ul>
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<li>Check the index aliases on AReS Explorer to make sure they are sane before starting a new harvest:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
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</code></pre><ul>
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<li>Then set the <code>openrxv-items-final</code> index to read-only so we can make a backup:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
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{"acknowledged":true}%
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$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-backup
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{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final-backup"}%
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$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
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</code></pre><ul>
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<li>Then start a harvesting on AReS Explorer</li>
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<li>Help Enrico get some 2020 statistics for the Roots, Tubers and Bananas (RTB) community on CGSpace
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<ul>
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<li>He was hitting <a href="https://github.com/ilri/OpenRXV/issues/66">a bug on AReS</a> and also he only needed stats for 2020, and AReS currently only gives all-time stats</li>
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</ul>
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</li>
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<li>I cleaned up about 230 ISSNs on CGSpace in OpenRefine
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<ul>
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<li>I had exported them last week, then filtered for anything not looking like an ISSN with this GREL: <code>isNotNull(value.match(/^\p{Alnum}{4}-\p{Alnum}{4}$/))</code></li>
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<li>Then I applied them on CGSpace with the <code>fix-metadata-values.py</code> script:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ ./ilri/fix-metadata-values.py -i /tmp/2021-04-01-ISSNs.csv -db dspace -u dspace -p 'fuuu' -f cg.issn -t 'correct' -m 253
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</code></pre><ul>
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<li>For now I only fixed obvious errors like “1234-5678.” and “e-ISSN: 1234-5678” etc, but there are still lots of invalid ones which need more manual work:
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<ul>
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<li>Too few characters</li>
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<li>Too many characters</li>
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<li>ISBNs</li>
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</ul>
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</li>
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<li>Create the CGSpace community and collection structure for the new Accelerating Impacts of CGIAR Climate Research for Africa (AICCRA) and assign all workflow steps</li>
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</ul>
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<h2 id="2021-04-04-1">2021-04-04</h2>
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<ul>
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<li>The AReS Explorer harvesting from yesterday finished, and the results look OK, but actually the Elasticsearch indexes are messed up again:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
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{
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"openrxv-items-final": {
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"aliases": {}
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},
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"openrxv-items-temp": {
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"aliases": {
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"openrxv-items": {}
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}
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},
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...
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}
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</code></pre><ul>
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<li><code>openrxv-items</code> should be an alias of <code>openrxv-items-final</code>, not <code>openrxv-temp</code>… I will have to fix that manually</li>
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<li>Enrico asked for more information on the RTB stats I gave him yesterday
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<ul>
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<li>I remembered (again) that we can’t filter Atmire’s CUA stats by date issued</li>
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<li>To show, for example, views/downloads in the year 2020 for RTB issued in 2020, we would need to use the DSpace statistics API and post a list of IDs and a custom date range</li>
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<li>I tried to do that here by exporting the RTB community and extracting the IDs for items issued in 2020:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ ~/dspace63/bin/dspace metadata-export -i 10568/80100 -f /tmp/rtb.csv
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$ csvcut -c 'id,dcterms.issued,dcterms.issued[],dcterms.issued[en_US]' /tmp/rtb.csv | \
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sed '1d' | \
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csvsql --no-header --no-inference --query 'SELECT a AS id,COALESCE(b, "")||COALESCE(c, "")||COALESCE(d, "") AS issued FROM stdin' | \
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csvgrep -c issued -m 2020 | \
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csvcut -c id | \
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sed '1d' | \
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sort | \
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uniq
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</code></pre><ul>
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<li>So I remember in the future, this basically does the following:
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<ul>
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<li>Use csvcut to extract the id and all date issued columns from the CSV</li>
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<li>Use sed to remove the header so we can refer to the columns using default a, b, c instead of their real names (which are tricky to match due to special characters)</li>
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<li>Use csvsql to concatenate the various date issued columns (coalescing where null)</li>
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<li>Use csvgrep to filter items by date issued in 2020</li>
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<li>Use csvcut to extract the id column</li>
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<li>Use sed to delete the header row</li>
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<li>Use sort and uniq to filter out any duplicate IDs (there were three)</li>
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</ul>
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</li>
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<li>Then I have a list of 296 IDs for RTB items issued in 2020</li>
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<li>I constructed a JSON file to post to the DSpace Statistics API:</li>
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</ul>
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<div class="highlight"><pre style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4"><code class="language-json" data-lang="json">{
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<span style="color:#f92672">"limit"</span>: <span style="color:#ae81ff">100</span>,
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<span style="color:#f92672">"page"</span>: <span style="color:#ae81ff">0</span>,
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<span style="color:#f92672">"dateFrom"</span>: <span style="color:#e6db74">"2020-01-01T00:00:00Z"</span>,
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<span style="color:#f92672">"dateTo"</span>: <span style="color:#e6db74">"2020-12-31T00:00:00Z"</span>,
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<span style="color:#f92672">"items"</span>: [
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<span style="color:#e6db74">"00358715-b70c-4fdd-aa55-730e05ba739e"</span>,
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<span style="color:#e6db74">"004b54bb-f16f-4cec-9fbc-ab6c6345c43d"</span>,
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<span style="color:#e6db74">"02fb7630-d71a-449e-b65d-32b4ea7d6904"</span>,
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<span style="color:#960050;background-color:#1e0010">...</span>
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]
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}
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</code></pre></div><ul>
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<li>Then I submitted the file three times (changing the page parameter):</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page1.json
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$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page2.json
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$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page3.json
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</code></pre><ul>
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<li>Then I extracted the views and downloads in the most ridiculous way:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ grep views /tmp/page*.json | grep -o -E '[0-9]+$' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
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30364
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$ grep downloads /tmp/page*.json | grep -o -E '[0-9]+,' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
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9100
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</code></pre><ul>
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<li>For curiousity I did the same exercise for items issued in 2019 and got the following:
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<ul>
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<li>Views: 30721</li>
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<li>Downloads: 10205</li>
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</ul>
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</li>
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</ul>
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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/2021-04/">April, 2021</a></li>
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<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
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<li><a href="/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></li>
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<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
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<li><a href="/cgspace-notes/2021-01/">January, 2021</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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