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Peter emailed to point out that many items in the ILRI archive collection have multiple handles:
http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine
2017-10-01 12:44:37 +02:00
Add Katherine Lutz to the groups for content sumission and edit steps of the CGIAR System collections
2017-10-01 07:13:31 +02:00
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Peter emailed to point out that many items in the ILRI archive collection have multiple handles:
http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine
2017-10-01 12:44:37 +02:00
Add Katherine Lutz to the groups for content sumission and edit steps of the CGIAR System collections
2017-10-01 07:13:31 +02:00
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<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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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54&#43;03:00">Sun Oct 01, 2017</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre>
<ul>
<li>There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li>
2017-10-01 12:44:37 +02:00
<li>Add Katherine Lutz to the groups for content sumission and edit steps of the CGIAR System collections</li>
2017-10-01 07:13:31 +02:00
</ul>
<p></p>
2017-10-02 07:14:44 +02:00
<h2 id="2017-10-02">2017-10-02</h2>
<ul>
<li>Peter Ballantyne said he was having problems logging into CGSpace with &ldquo;both&rdquo; of his accounts (CGIAR LDAP and personal, apparently)</li>
<li>I looked in the logs and saw some LDAP lookup failures due to timeout but also strangely a &ldquo;no DN found&rdquo; error:</li>
</ul>
<pre><code>2017-10-01 20:24:57,928 WARN org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=CA0AA5FEAEA8805645489404CDCE9594:ip_addr=41.204.190.40:ldap_attribute_lookup:type=failed_search javax.naming.CommunicationException\colon; svcgroot2.cgiarad.org\colon;3269 [Root exception is java.net.ConnectException\colon; Connection timed out (Connection timed out)]
2017-10-01 20:22:37,982 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=CA0AA5FEAEA8805645489404CDCE9594:ip_addr=41.204.190.40:failed_login:no DN found for user pballantyne
</code></pre>
<ul>
2017-10-02 07:31:19 +02:00
<li>I thought maybe his account had expired (seeing as it&rsquo;s was the first of the month) but he says he was finally able to log in today</li>
<li>The logs for yesterday show fourteen errors related to LDAP auth failures:</li>
</ul>
<pre><code>$ grep -c &quot;ldap_authentication:type=failed_auth&quot; dspace.log.2017-10-01
14
</code></pre>
<ul>
<li>For what it&rsquo;s worth, there are no errors on any other recent days, so it must have been some network issue on Linode or CGNET&rsquo;s LDAP server</li>
2017-10-02 16:29:23 +02:00
<li>Linode emailed to say that linode578611 (DSpace Test) needs to migrate to a new host for a security update so I initiated the migration immediately rather than waiting for the scheduled time in two weeks</li>
2017-10-02 07:14:44 +02:00
</ul>
2017-10-04 10:29:41 +02:00
<h2 id="2017-10-04">2017-10-04</h2>
<ul>
<li>Twice in the last twenty-four hours Linode has alerted about high CPU usage on CGSpace (linode2533629)</li>
<li>Communicate with Sam from the CGIAR System Organization about some broken links coming from their CGIAR Library domain to CGSpace</li>
<li>The first is a link to a browse page that should be handled better in nginx:</li>
</ul>
<pre><code>http://library.cgiar.org/browse?value=Intellectual%20Assets%20Reports&amp;type=subject → https://cgspace.cgiar.org/browse?value=Intellectual%20Assets%20Reports&amp;type=subject
</code></pre>
<ul>
<li>We&rsquo;ll need to check for browse links and handle them properly, including swapping the <code>subject</code> parameter for <code>systemsubject</code> (which doesn&rsquo;t exist in Discovery yet, but we&rsquo;ll need to add it) as we have moved their poorly curated subjects from <code>dc.subject</code> to <code>cg.subject.system</code></li>
<li>The second link was a direct link to a bitstream which has broken due to the sequence being updated, so I told him he should link to the handle of the item instead</li>
2017-10-04 14:56:39 +02:00
<li>Help Sisay proof sixty-two IITA records on DSpace Test</li>
<li>Lots of inconsistencies and errors in subjects, dc.format.extent, regions, countries</li>
2017-10-04 16:06:10 +02:00
<li>Merge the Discovery search changes for ISI Journal (<a href="https://github.com/ilri/DSpace/pull/341">#341</a>)</li>
2017-10-04 10:29:41 +02:00
</ul>
2017-10-05 17:36:49 +02:00
<h2 id="2017-10-05">2017-10-05</h2>
<ul>
<li>Twice in the past twenty-four hours Linode has warned that CGSpace&rsquo;s outbound traffic rate was exceeding the notification threshold</li>
<li>I had a look at yesterday&rsquo;s OAI and REST logs in <code>/var/log/nginx</code> but didn&rsquo;t see anything unusual:</li>
</ul>
<pre><code># awk '{print $1}' /var/log/nginx/rest.log.1 | sort -n | uniq -c | sort -h | tail -n 10
141 157.55.39.240
145 40.77.167.85
162 66.249.66.92
181 66.249.66.95
211 66.249.66.91
312 66.249.66.94
384 66.249.66.90
1495 50.116.102.77
3904 70.32.83.92
9904 45.5.184.196
# awk '{print $1}' /var/log/nginx/oai.log.1 | sort -n | uniq -c | sort -h | tail -n 10
5 66.249.66.71
6 66.249.66.67
6 68.180.229.31
8 41.84.227.85
8 66.249.66.92
17 66.249.66.65
24 66.249.66.91
38 66.249.66.95
69 66.249.66.90
148 66.249.66.94
</code></pre>
<ul>
<li>Working on the nginx redirects for CGIAR Library</li>
<li>We should start using 301 redirects and also allow for <code>/sitemap</code> to work on the library.cgiar.org domain so the CGIAR System Organization people can update their Google Search Console and allow Google to find their content in a structured way</li>
<li>Remove eleven occurrences of <code>ACP</code> in IITA&rsquo;s <code>cg.coverage.region</code> using the Atmire batch edit module from Discovery</li>
<li>Need to investigate how we can verify the library.cgiar.org using the HTML or DNS methods</li>
2017-10-06 02:10:53 +02:00
<li>Run corrections on 143 ILRI Archive items that had two <code>dc.identifier.uri</code> values (Handle) that Peter had pointed out earlier this week</li>
<li>I used OpenRefine to isolate them and then fixed and re-imported them into CGSpace</li>
2017-10-06 02:11:56 +02:00
<li>I manually checked a dozen of them and it appeared that the correct handle was always the second one, so I just deleted the first one</li>
2017-10-05 17:36:49 +02:00
</ul>
2017-10-06 11:22:46 +02:00
<h2 id="2017-10-06">2017-10-06</h2>
<ul>
<li>I saw a nice tweak to thumbnail presentation on the Cardiff Metropolitan University DSpace: <a href="https://repository.cardiffmet.ac.uk/handle/10369/8780">https://repository.cardiffmet.ac.uk/handle/10369/8780</a></li>
<li>It adds a subtle border and box shadow, before and after:</li>
</ul>
<p><img src="/cgspace-notes/2017/10/dspace-thumbnail-original.png" alt="Original flat thumbnails" />
<img src="/cgspace-notes/2017/10/dspace-thumbnail-box-shadow.png" alt="Tweaked with border and box shadow" /></p>
<ul>
<li>I&rsquo;ll post it to the Yammer group to see what people think</li>
2017-10-06 18:27:58 +02:00
<li>I figured out at way to do the HTML verification for Google Search console for library.cgiar.org</li>
<li>We can drop the HTML file in their XMLUI theme folder and it will get copied to the webapps directory during build/install</li>
<li>Then we add an nginx alias for that URL in the library.cgiar.org vhost</li>
<li>This method is kinda a hack but at least we can put all the pieces into git to be reproducible</li>
<li>I will tell Tunji to send me the verification file</li>
2017-10-06 11:22:46 +02:00
</ul>
2017-10-10 13:22:54 +02:00
<h2 id="2017-10-10">2017-10-10</h2>
<ul>
<li>Deploy logic to allow verification of the library.cgiar.org domain in the Google Search Console (<a href="https://github.com/ilri/DSpace/pull/343">#343</a>)</li>
<li>After verifying both the HTTP and HTTPS domains and submitting a sitemap it will be interesting to see how the stats in the console as well as the search results change (currently 28,500 results):</li>
</ul>
<p><img src="/cgspace-notes/2017/10/google-search-console.png" alt="Google Search Console" />
<img src="/cgspace-notes/2017/10/google-search-console-2.png" alt="Google Search Console 2" />
<img src="/cgspace-notes/2017/10/google-search-results.png" alt="Google Search results" /></p>
<ul>
<li>I tried to submit a &ldquo;Change of Address&rdquo; request in the Google Search Console but I need to be an owner on CGSpace&rsquo;s console (currently I&rsquo;m just a user) in order to do that</li>
2017-10-11 01:21:51 +02:00
<li>Manually clean up some communities and collections that Peter had requested a few weeks ago</li>
<li>Delete Community <sup>10568</sup>&frasl;<sub>102</sub> (ILRI Research and Development Issues)</li>
<li>Move five collections to <sup>10568</sup>&frasl;<sub>27629</sub> (ILRI Projects) using <code>move-collections.sh</code> with the following configuration:</li>
</ul>
<pre><code>10568/1637 10568/174 10568/27629
10568/1642 10568/174 10568/27629
10568/1614 10568/174 10568/27629
10568/75561 10568/150 10568/27629
10568/183 10568/230 10568/27629
</code></pre>
<ul>
<li>Delete community <sup>10568</sup>&frasl;<sub>174</sub> (Sustainable livestock futures)</li>
<li>Delete collections in <sup>10568</sup>&frasl;<sub>27629</sub> that have zero items (33 of them!)</li>
2017-10-10 13:22:54 +02:00
</ul>
2017-10-11 12:58:31 +02:00
<h2 id="2017-10-11">2017-10-11</h2>
<ul>
<li>Peter added me as an owner on the CGSpace property on Google Search Console and I tried to submit a &ldquo;Change of Address&rdquo; request for the CGIAR Library but got an error:</li>
</ul>
<p><img src="/cgspace-notes/2017/10/search-console-change-address-error.png" alt="Change of Address error" /></p>
<ul>
<li>We are sending top-level CGIAR Library traffic to their specific community hierarchy in CGSpace so this type of change of address won&rsquo;t work—we&rsquo;ll just need to wait for Google to slowly index everything and take note of the HTTP 301 redirects</li>
<li>Also the Google Search Console doesn&rsquo;t work very well with Google Analytics being blocked, so I had to turn off my ad blocker to get the &ldquo;Change of Address&rdquo; tool to work!</li>
</ul>
2017-10-13 01:37:59 +02:00
<h2 id="2017-10-12">2017-10-12</h2>
<ul>
<li>Finally finish (I think) working on the myriad nginx redirects for all the CGIAR Library browse stuff—it ended up getting pretty complicated!</li>
<li>I still need to commit the DSpace changes (add browse index, XMLUI strings, Discovery index, etc), but I should be able to deploy that on CGSpace soon</li>
</ul>
2017-10-14 14:30:51 +02:00
<h2 id="2017-10-14">2017-10-14</h2>
<ul>
<li>Run system updates on DSpace Test and reboot server</li>
<li>Merge changes adding a search/browse index for CGIAR System subject to <code>5_x-prod</code> (<a href="https://github.com/ilri/DSpace/pull/344">#344</a>)</li>
<li>I checked the top browse links in Google&rsquo;s search results for <code>site:library.cgiar.org inurl:browse</code> and they are all redirected appropriately by the nginx rewrites I worked on last week</li>
</ul>
2017-10-22 22:51:48 +02:00
<h2 id="2017-10-22">2017-10-22</h2>
<ul>
<li>Run system updates on DSpace Test and reboot server</li>
<li>Re-deploy CGSpace from latest <code>5_x-prod</code> (adds ISI Journal to search filters and adds Discovery index for CGIAR Library <code>systemsubject</code>)</li>
<li>Deploy nginx redirect fixes to catch CGIAR Library browse links (redirect to their community and translate subject→systemsubject)</li>
2017-10-23 08:58:33 +02:00
<li>Run migration of CGSpace server (linode18) for Linode security alert, which took 42 minutes of downtime</li>
2017-10-22 22:51:48 +02:00
</ul>
2017-10-26 16:23:36 +02:00
<h2 id="2017-10-26">2017-10-26</h2>
<ul>
<li>In the last 24 hours we&rsquo;ve gotten a few alerts from Linode that there was high CPU and outgoing traffic on CGSpace</li>
<li>Uptime Robot even noticed CGSpace go &ldquo;down&rdquo; for a few minutes</li>
<li>In other news, I was trying to look at a question about stats raised by Magdalena and then CGSpace went down due to SQL connection pool</li>
<li>Looking at the PostgreSQL activity I see there are 93 connections, but after a minute or two they went down and CGSpace came back up</li>
<li>Annnd I reloaded the Atmire Usage Stats module and the connections shot back up and CGSpace went down again</li>
<li>Still not sure where the load is coming from right now, but it&rsquo;s clear why there were so many alerts yesterday on the 25th!</li>
</ul>
<pre><code># grep -o -E 'session_id=[A-Z0-9]{32}' dspace.log.2017-10-25 | sort -n | uniq | wc -l
18022
</code></pre>
<ul>
<li>Compared to other days there were two or three times the number of requests yesterday!</li>
</ul>
<pre><code># grep -o -E 'session_id=[A-Z0-9]{32}' dspace.log.2017-10-23 | sort -n | uniq | wc -l
3141
# grep -o -E 'session_id=[A-Z0-9]{32}' dspace.log.2017-10-26 | sort -n | uniq | wc -l
7851
</code></pre>
<ul>
<li>I still have no idea what was causing the load to go up today</li>
<li>I finally investigated Magdalena&rsquo;s issue with the item download stats and now I can&rsquo;t reproduce it: I get the same number of downloads reported in the stats widget on the item page, the &ldquo;Most Popular Items&rdquo; page, and in Usage Stats</li>
<li>I think it might have been an issue with the statistics not being fresh</li>
2017-10-26 16:50:10 +02:00
<li>I added the admin group for the systems organization to the admin role of the top-level community of CGSpace because I guess Sisay had forgotten</li>
<li>Magdalena asked if there was a way to reuse data in item submissions where items have a lot of similar data</li>
<li>I told her about the possibility to use per-collection item templates, and asked if her items in question were all from a single collection</li>
<li>We&rsquo;ve never used it but it could be worth looking at</li>
2017-10-26 16:23:36 +02:00
</ul>
2017-10-28 11:31:47 +02:00
<h2 id="2017-10-27">2017-10-27</h2>
<ul>
<li>Linode alerted about high CPU usage again (twice) on CGSpace in the last 24 hours, around 2AM and 2PM</li>
</ul>
<h2 id="2017-10-28">2017-10-28</h2>
<ul>
<li>Linode alerted about high CPU usage again on CGSpace around 2AM this morning</li>
</ul>
2017-10-29 09:02:34 +01:00
<h2 id="2017-10-29">2017-10-29</h2>
<ul>
<li>Linode alerted about high CPU usage again on CGSpace around 2AM and 4AM</li>
<li>I&rsquo;m still not sure why this started causing alerts so repeatadely the past week</li>
<li>I don&rsquo;t see any tell tale signs in the REST or OAI logs, so trying to do rudimentary analysis in DSpace logs:</li>
</ul>
<pre><code># grep '2017-10-29 02:' dspace.log.2017-10-29 | grep -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
2049
</code></pre>
<ul>
<li>So there were 2049 unique sessions during the hour of 2AM</li>
<li>Looking at my notes, the number of unique sessions was about the same during the same hour on other days when there were no alerts</li>
<li>I think I&rsquo;ll need to enable access logging in nginx to figure out what&rsquo;s going on</li>
<li>After enabling logging on requests to XMLUI on <code>/</code> I see some new bot I&rsquo;ve never seen before:</li>
</ul>
<pre><code>137.108.70.6 - - [29/Oct/2017:07:39:49 +0000] &quot;GET /discover?filtertype_0=type&amp;filter_relational_operator_0=equals&amp;filter_0=Internal+Document&amp;filtertype=author&amp;filter_relational_operator=equals&amp;filter=CGIAR+Secretariat HTTP/1.1&quot; 200 7776 &quot;-&quot; &quot;Mozilla/5.0 (compatible; CORE/0.6; +http://core.ac.uk; http://core.ac.uk/intro/contact)&quot;
</code></pre>
<ul>
<li>CORE seems to be some bot that is &ldquo;Aggregating the worlds open access research papers&rdquo;</li>
<li>The contact address listed in their bot&rsquo;s user agent is incorrect, correct page is simply: <a href="https://core.ac.uk/contact">https://core.ac.uk/contact</a></li>
<li>I will check the logs in a few days to see if they are harvesting us regularly, then add their bot&rsquo;s user agent to the Tomcat Crawler Session Valve</li>
<li>After browsing the CORE site it seems that the CGIAR Library is somehow a member of CORE, so they have probably only been harvesting CGSpace since we did the migration, as library.cgiar.org directs to us now</li>
<li>For now I will just contact them to have them update their contact info in the bot&rsquo;s user agent, but eventually I think I&rsquo;ll tell them to swap out the CGIAR Library entry for CGSpace</li>
</ul>
2017-10-30 17:01:05 +01:00
<h2 id="2017-10-30">2017-10-30</h2>
<ul>
<li>Like clock work, Linode alerted about high CPU usage on CGSpace again this morning (this time at 8:13 AM)</li>
<li>Uptime Robot noticed that CGSpace went down around 10:15 AM, and I saw that there were 93 PostgreSQL connections:</li>
</ul>
<pre><code>dspace=# SELECT * FROM pg_stat_activity;
...
(93 rows)
</code></pre>
<ul>
<li>Surprise surprise, the CORE bot is likely responsible for the recent load issues, making hundreds of thousands of requests yesterday and today:</li>
</ul>
<pre><code># grep -c &quot;CORE/0.6&quot; /var/log/nginx/access.log
26475
# grep -c &quot;CORE/0.6&quot; /var/log/nginx/access.log.1
135083
</code></pre>
<ul>
<li>IP addresses for this bot currently seem to be:</li>
</ul>
<pre><code># grep &quot;CORE/0.6&quot; /var/log/nginx/access.log | awk '{print $1}' | sort -n | uniq
137.108.70.6
137.108.70.7
</code></pre>
<ul>
<li>I will add their user agent to the Tomcat Session Crawler Valve but it won&rsquo;t help much because they are only using two sessions:</li>
</ul>
<pre><code># grep 137.108.70 dspace.log.2017-10-30 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq
session_id=5771742CABA3D0780860B8DA81E0551B
session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
</code></pre>
<ul>
<li>&hellip; and most of their requests are for dynamic discover pages:</li>
</ul>
<pre><code># grep -c 137.108.70 /var/log/nginx/access.log
26622
# grep 137.108.70 /var/log/nginx/access.log | grep -c &quot;GET /discover&quot;
24055
</code></pre>
<ul>
<li>Just because I&rsquo;m curious who the top IPs are:</li>
</ul>
<pre><code># awk '{print $1}' /var/log/nginx/access.log | sort -n | uniq -c | sort -h | tail
496 62.210.247.93
571 46.4.94.226
651 40.77.167.39
763 157.55.39.231
782 207.46.13.90
998 66.249.66.90
1948 104.196.152.243
4247 190.19.92.5
31602 137.108.70.6
31636 137.108.70.7
</code></pre>
<ul>
<li>At least we know the top two are CORE, but who are the others?</li>
<li>190.19.92.5 is apparently in Argentina, and 104.196.152.243 is from Google Cloud Engine</li>
<li>Actually, these two scrapers might be more responsible for the heavy load than the CORE bot, because they don&rsquo;t reuse their session variable, creating thousands of new sessions!</li>
</ul>
<pre><code># grep 190.19.92.5 dspace.log.2017-10-30 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
1419
# grep 104.196.152.243 dspace.log.2017-10-30 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
2811
</code></pre>
<ul>
<li>From looking at the requests, it appears these are from CIAT and CCAFS</li>
<li>I wonder if I could somehow instruct them to use a user agent so that we could apply a crawler session manager valve to them</li>
<li>Actually, according to the Tomcat docs, we could use an IP with <code>crawlerIps</code>: <a href="https://tomcat.apache.org/tomcat-7.0-doc/config/valve.html#Crawler_Session_Manager_Valve">https://tomcat.apache.org/tomcat-7.0-doc/config/valve.html#Crawler_Session_Manager_Valve</a></li>
2017-10-30 17:45:35 +01:00
<li>Ah, wait, it looks like <code>crawlerIps</code> only came in 2017-06, so probably isn&rsquo;t in Ubuntu 16.04&rsquo;s 7.0.68 build!</li>
<li>That would explain the errors I was getting when trying to set it:</li>
</ul>
<pre><code>WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Valve} Setting property 'crawlerIps' to '190\.19\.92\.5|104\.196\.152\.243' did not find a matching property.
</code></pre>
<ul>
2017-10-30 17:01:05 +01:00
<li>As for now, it actually seems the CORE bot coming from 137.108.70.6 and 137.108.70.7 is only using a few sessions per day, which is good:</li>
</ul>
<pre><code># grep -o -E 'session_id=[A-Z0-9]{32}:ip_addr=137.108.70.(6|7)' dspace.log.2017-10-30 | sort -n | uniq -c | sort -h
410 session_id=74F0C3A133DBF1132E7EC30A7E7E0D60:ip_addr=137.108.70.7
574 session_id=5771742CABA3D0780860B8DA81E0551B:ip_addr=137.108.70.7
1012 session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A:ip_addr=137.108.70.6
</code></pre>
<ul>
<li>I will check again tomorrow</li>
</ul>
2017-10-01 07:13:31 +02:00
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