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<meta property="og:description" content="2020-05-02
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Peter said that CTA is having problems submitting an item to CGSpace
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Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in ‘idle in transaction’ and ‘waiting for lock’ state are increasing again
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I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)
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<meta name="twitter:description" content="2020-05-02
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Peter said that CTA is having problems submitting an item to CGSpace
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Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in ‘idle in transaction’ and ‘waiting for lock’ state are increasing again
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I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)
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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/2020-05/">May, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-05-02T09:52:04+03:00">Sat May 02, 2020</time> by Alan Orth 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="2020-05-02">2020-05-02</h2>
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<ul>
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<li>Peter said that CTA is having problems submitting an item to CGSpace
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<ul>
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<li>Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in ‘idle in transaction’ and ‘waiting for lock’ state are increasing again</li>
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<li>I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-05-03">2020-05-03</h2>
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<ul>
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<li>Purge a few remaining bots from CGSpace Solr statistics that I had identified a few months ago
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<ul>
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<li><code>lua-resty-http/0.10 (Lua) ngx_lua/10000</code></li>
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<li><code>omgili/0.5 +http://omgili.com</code></li>
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<li><code>IZaBEE/IZaBEE-1.01 (Buzzing Abound The Web; https://izabee.com; info at izabee dot com)</code></li>
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<li><code>Twurly v1.1 (https://twurly.org)</code></li>
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<li><code>Pattern/2.6 +http://www.clips.ua.ac.be/pattern</code></li>
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<li><code>CyotekWebCopy/1.7 CyotekHTTP/2.0</code></li>
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</ul>
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</li>
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<li>This is only about 2,500 hits total from the last ten years, and half of these bots no longer seem to exist, so I won’t bother submitting them to the COUNTER-Robots project</li>
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<li>I noticed that our custom themes were incorrectly linking to the OpenSearch XML file
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<ul>
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<li>The bug <a href="https://jira.lyrasis.org/browse/DS-2592">was fixed</a> for Mirage2 in 2015</li>
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<li>Note that this did not prevent OpenSearch itself from working</li>
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<li>I will patch this on our DSpace 5.x and 6.x branches</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-05-06">2020-05-06</h2>
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<ul>
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<li>Atmire responded asking for more information about the Solr statistics processing bug in CUA so I sent them some full logs
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<ul>
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<li>Also I asked again about the Maven variable interpolation issue for <code>cua.version.number</code>, and if they would be willing to upgrade CUA to use Font Awesome 5 instead of 4.</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-05-07">2020-05-07</h2>
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<ul>
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<li>Linode sent an alert that there was high CPU usage on CGSpace (linode18) early this morning
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<ul>
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<li>I looked at the nginx logs using goaccess and I found a few IPs making lots of requests around then:</li>
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</ul>
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</li>
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</ul>
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<pre><code># cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "07/May/2020:(01|03|04)" | goaccess --log-format=COMBINED -
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</code></pre><ul>
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<li>The two main IPs making requests around then are 188.134.31.88 and 212.34.8.188
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<ul>
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<li>The first is in Russia and it is hitting mostly XMLUI Discover links using <em>dozens</em> of different user agents, a total of 20,000 requests this week</li>
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<li>The second IP is CodeObia testing AReS, a total of 171,000 hits this month</li>
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<li>I will purge both of those IPs from the Solr stats using my <code>check-spider-ip-hits.sh</code> script:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ ./check-spider-ip-hits.sh -f /tmp/ips -s statistics -p
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Purging 171641 hits from 212.34.8.188 in statistics
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Purging 20691 hits from 188.134.31.88 in statistics
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Total number of bot hits purged: 192332
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</code></pre><ul>
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<li>And then I will add 188.134.31.88 to the nginx bad bot list and tell CodeObia to please use a “bot” user agent</li>
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<li>I also changed the nginx config to block requests with blank user agents</li>
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</ul>
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<h2 id="2020-05-11">2020-05-11</h2>
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<ul>
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<li>Bizu said she was having issues submitting to CGSpace last week
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<ul>
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<li>The issue sounds like the one Tezira and CTA were having in the last few weeks</li>
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<li>I looked at the PostgreSQL graphs and see there are a lot of connections in “idle in transaction” and “waiting for lock” state:</li>
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</ul>
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</li>
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</ul>
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<p><img src="/cgspace-notes/2020/05/postgres_connections_cgspace-week.png" alt="PostgreSQL connections"></p>
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<ul>
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<li>I think I’ll downgrade the PostgreSQL JDBC driver from 42.2.12 to 42.2.10, which was the version we were using before these issues started happening</li>
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<li>Atmire sent some feedback about my ongoing issues with their CUA module, but none of it was conclusive yet
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<ul>
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<li>Regarding Font Awesome 5 they will check how much work it will take and give me a quote</li>
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</ul>
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</li>
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<li>Abenet said some users are questioning why the statistics dropped so much lately, so I made a <a href="https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=674923030216704">post to Yammer</a> to explain about the robots</li>
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<li>Last week Peter had asked me to add a new ILRI author’s ORCID iD
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<ul>
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<li>I added it to the controlled vocabulary and tagged the user’s existing ~11 items in CGSpace using this CSV file with my <code>add-orcid-identifiers-csv.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>$ cat 2020-05-11-add-orcids.csv
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dc.contributor.author,cg.creator.id
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"Lutakome, P.","Pius Lutakome: 0000-0002-0804-2649"
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"Lutakome, Pius","Pius Lutakome: 0000-0002-0804-2649"
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$ ./add-orcid-identifiers-csv.py -i 2020-05-11-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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</code></pre><ul>
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<li>Run system updates on CGSpace (linode18) and reboot it
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<ul>
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<li>I had to restart Tomcat five times before all Solr statistics cores came up OK, ugh.</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-05-12">2020-05-12</h2>
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<ul>
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<li>Peter noticed that CGSpace is no longer on AReS, because I blocked all requests that don’t specify a user agent
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<ul>
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<li>I’ve temporarily disabled that restriction and asked Moayad to look into how he can specify a user agent in the AReS harvester</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-05-13">2020-05-13</h2>
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<ul>
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<li>Atmire responded about Font Awesome and said they can switch to version 5 for 16 credits
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<ul>
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<li>I told them to go ahead</li>
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</ul>
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</li>
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<li>Also, Atmire gave me a small workaround for the <code>cua.version.number</code> interpolation issue and said they would look into the crash that happens when processing our Solr stats</li>
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<li>Run system updates and reboot AReS server (linode20) for the first time in almost 100 days
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<ul>
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<li>I notice that AReS now has some of CGSpace’s data in it (but not all) since I dropped the user-agent restriction on the REST API yesterday</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-05-17">2020-05-17</h2>
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<ul>
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<li>Create an issue in the OpenRXV project for Moayad to change the default harvester user agent (<a href="https://github.com/ilri/OpenRXV/issues/36">#36</a>)</li>
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</ul>
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<h2 id="2020-05-18">2020-05-18</h2>
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<ul>
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<li>Atmire responded and said they still can’t figure out the CUA statistics issue, though they seem to only be trying to understand what’s going on using static analysis
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<ul>
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<li>I told them that they should try to run the code with the Solr statistics that I shared with them a few weeks ago</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-05-19">2020-05-19</h2>
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<ul>
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<li>Add ORCID identifier for Sirak Bahta
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<ul>
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<li>I added it to the controlled vocabulary and tagged the user’s existing ~40 items in CGSpace using this CSV file with my <code>add-orcid-identifiers-csv.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>$ cat 2020-05-19-add-orcids.csv
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dc.contributor.author,cg.creator.id
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$ ./add-orcid-identifiers-csv.py -i 2020-05-19-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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"Bahta, Sirak T.","Sirak Bahta: 0000-0002-5728-2489"
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</code></pre><!-- raw HTML omitted -->
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</article>
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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/2020-05/">May, 2020</a></li>
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<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
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<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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<li><a href="/cgspace-notes/2020-01/">January, 2020</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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