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Alan Orth
2022-03-04 15:30:06 +03:00
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@ -36,7 +36,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r
There is insufficient memory for the Java Runtime Environment to continue.
"/>
<meta name="generator" content="Hugo 0.92.2" />
<meta name="generator" content="Hugo 0.93.1" />
@ -134,7 +134,7 @@ There is insufficient memory for the Java Runtime Environment to continue.
</code></pre><ul>
<li>As the machine only has 8GB of RAM, I reduced the Tomcat memory heap from 5120m to 4096m so I could try to allocate more to the build process:</li>
</ul>
<pre tabindex="0"><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx1024m&quot;
<pre tabindex="0"><code>$ export JAVA_OPTS=&#34;-Dfile.encoding=UTF-8 -Xmx1024m&#34;
$ mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -Denv=dspacetest.cgiar.org -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2 clean package
</code></pre><ul>
<li>Then I stopped the Tomcat 7 service, ran the ant update, and manually ran the old and ignored SQL migrations:</li>
@ -171,17 +171,17 @@ $ dspace database migrate ignored
</ul>
</li>
</ul>
<pre tabindex="0"><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx1024m&quot;
<pre tabindex="0"><code>$ export JAVA_OPTS=&#34;-Dfile.encoding=UTF-8 -Xmx1024m&#34;
$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive.csv
$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive2.csv
</code></pre><ul>
<li>I noticed there are many items that use HTTP instead of HTTPS for their Google Books URL, and some missing HTTP entirely:</li>
</ul>
<pre tabindex="0"><code>dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
<pre tabindex="0"><code>dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value like &#39;http://books.google.%&#39;;
count
-------
785
dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value ~ &#39;^books\.google\..*&#39;;
count
-------
4
@ -189,11 +189,11 @@ dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadat
<li>I think I should fix that as well as some other garbage values like &ldquo;test&rdquo; and &ldquo;dspace.ilri.org&rdquo; etc:</li>
</ul>
<pre tabindex="0"><code>dspace=# begin;
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
dspace=# update metadatavalue set text_value = regexp_replace(text_value, &#39;http://books.google&#39;, &#39;https://books.google&#39;) where resource_type_id=2 and metadata_field_id=222 and text_value like &#39;http://books.google.%&#39;;
UPDATE 785
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
dspace=# update metadatavalue set text_value = regexp_replace(text_value, &#39;books.google&#39;, &#39;https://books.google&#39;) where resource_type_id=2 and metadata_field_id=222 and text_value ~ &#39;^books\.google\..*&#39;;
UPDATE 4
dspace=# update metadatavalue set text_value='https://books.google.com/books?id=meF1CLdPSF4C' where resource_type_id=2 and metadata_field_id=222 and text_value='meF1CLdPSF4C';
dspace=# update metadatavalue set text_value=&#39;https://books.google.com/books?id=meF1CLdPSF4C&#39; where resource_type_id=2 and metadata_field_id=222 and text_value=&#39;meF1CLdPSF4C&#39;;
UPDATE 1
dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=222 and metadata_value_id in (2299312, 10684, 10700, 996403);
DELETE 4
@ -202,7 +202,7 @@ dspace=# commit;
<li>Testing DSpace 5.8 with PostgreSQL 9.6 and Tomcat 8.5.32 (instead of my usual 7.0.88) and for some reason I get autowire errors on Catalina startup with 8.5.32:</li>
</ul>
<pre tabindex="0"><code>03-Jul-2018 19:51:37.272 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener]
java.lang.RuntimeException: Failure during filter init: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
java.lang.RuntimeException: Failure during filter init: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name &#39;conversionService&#39; defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean &#39;com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a&#39; of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property &#39;converters&#39; with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name &#39;com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a&#39;: Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
at org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener.contextInitialized(DSpaceKernelServletContextListener.java:92)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)
@ -217,7 +217,7 @@ dspace=# commit;
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name &#39;conversionService&#39; defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean &#39;com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a&#39; of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property &#39;converters&#39; with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name &#39;com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a&#39;: Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
</code></pre><ul>
<li>Gotta check that out later&hellip;</li>
</ul>
@ -249,7 +249,7 @@ Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Mana
<li>Abenet wants to be able to search by journal title (dc.source) in the advanced Discovery search so I opened an issue for it (<a href="https://github.com/ilri/DSpace/issues/384">#384</a>)</li>
<li>I regenerated the list of names for all our ORCID iDs using my <a href="https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b">resolve-orcids.py</a> script:</li>
</ul>
<pre tabindex="0"><code>$ grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml | sort | uniq &gt; /tmp/2018-07-08-orcids.txt
<pre tabindex="0"><code>$ grep -oE &#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39; ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml | sort | uniq &gt; /tmp/2018-07-08-orcids.txt
$ ./resolve-orcids.py -i /tmp/2018-07-08-orcids.txt -o /tmp/2018-07-08-names.txt -d
</code></pre><ul>
<li>But after comparing to the existing list of names I didn&rsquo;t see much change, so I just ignored it</li>
@ -259,7 +259,7 @@ $ ./resolve-orcids.py -i /tmp/2018-07-08-orcids.txt -o /tmp/2018-07-08-names.txt
<li>Uptime Robot said that CGSpace was down for two minutes early this morning but I don&rsquo;t see anything in Tomcat logs or dmesg</li>
<li>Uptime Robot said that CGSpace was down for two minutes again later in the day, and this time I saw a memory error in Tomcat&rsquo;s <code>catalina.out</code>:</li>
</ul>
<pre tabindex="0"><code>Exception in thread &quot;http-bio-127.0.0.1-8081-exec-557&quot; java.lang.OutOfMemoryError: Java heap space
<pre tabindex="0"><code>Exception in thread &#34;http-bio-127.0.0.1-8081-exec-557&#34; java.lang.OutOfMemoryError: Java heap space
</code></pre><ul>
<li>I&rsquo;m not sure if it&rsquo;s the same error, but I see this in DSpace&rsquo;s <code>solr.log</code>:</li>
</ul>
@ -274,7 +274,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
<li>I got a message from Linode tonight that CPU usage was high on CGSpace for the past few hours around 8PM GMT</li>
<li>Looking in the nginx logs I see the top ten IP addresses active today:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;09/Jul/2018&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;09/Jul/2018&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
1691 40.77.167.84
1701 40.77.167.69
1718 50.116.102.77
@ -288,7 +288,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
</code></pre><ul>
<li>Of those, <em>all</em> except <code>70.32.83.92</code> and <code>50.116.102.77</code> are <em>NOT</em> re-using their Tomcat sessions, for example from the XMLUI logs:</li>
</ul>
<pre tabindex="0"><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=95.108.181.88' dspace.log.2018-07-09
<pre tabindex="0"><code>$ grep -c -E &#39;session_id=[A-Z0-9]{32}:ip_addr=95.108.181.88&#39; dspace.log.2018-07-09
4435
</code></pre><ul>
<li><code>95.108.181.88</code> appears to be Yandex, so I dunno why it&rsquo;s creating so many sessions, as its user agent should match Tomcat&rsquo;s Crawler Session Manager Valve</li>
@ -314,7 +314,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
<li>Linode sent an alert about CPU usage on CGSpace again, about 13:00UTC</li>
<li>These are the top ten users in the last two hours:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;10/Jul/2018:(11|12|13)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;10/Jul/2018:(11|12|13)&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
81 193.95.22.113
82 50.116.102.77
112 40.77.167.90
@ -328,7 +328,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
</code></pre><ul>
<li>Looks like <code>213.139.52.250</code> is Moayad testing his new CGSpace vizualization thing:</li>
</ul>
<pre tabindex="0"><code>213.139.52.250 - - [10/Jul/2018:13:39:41 +0000] &quot;GET /bitstream/handle/10568/75668/dryad.png HTTP/2.0&quot; 200 53750 &quot;http://localhost:4200/&quot; &quot;Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/67.0.3396.87 Safari/537.36&quot;
<pre tabindex="0"><code>213.139.52.250 - - [10/Jul/2018:13:39:41 +0000] &#34;GET /bitstream/handle/10568/75668/dryad.png HTTP/2.0&#34; 200 53750 &#34;http://localhost:4200/&#34; &#34;Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/67.0.3396.87 Safari/537.36&#34;
</code></pre><ul>
<li>He said there was a bug that caused his app to request a bunch of invalid URLs</li>
<li>I&rsquo;ll have to keep and eye on this and see how their platform evolves</li>
@ -349,7 +349,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
<li>Uptime Robot said that CGSpace went down a few times last night, around 10:45 PM and 12:30 AM</li>
<li>Here are the top ten IPs from last night and this morning:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;11/Jul/2018:22&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;11/Jul/2018:22&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
48 66.249.64.91
50 35.227.26.162
57 157.55.39.234
@ -360,7 +360,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
97 183.128.40.185
97 240e:f0:44:fa53:745a:8afe:d221:1232
3634 208.110.72.10
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;12/Jul/2018:00&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;12/Jul/2018:00&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
25 216.244.66.198
38 40.77.167.185
46 66.249.64.93
@ -377,21 +377,21 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
<li>A brief Google search doesn&rsquo;t turn up any information about what this bot is, but lots of users complaining about it</li>
<li>This bot does make a lot of requests all through the day, although it seems to re-use its Tomcat session:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;Pcore-HTTP&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;Pcore-HTTP&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
17098 208.110.72.10
# grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=208.110.72.10' dspace.log.2018-07-11
# grep -c -E &#39;session_id=[A-Z0-9]{32}:ip_addr=208.110.72.10&#39; dspace.log.2018-07-11
1161
# grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=208.110.72.10' dspace.log.2018-07-12
# grep -c -E &#39;session_id=[A-Z0-9]{32}:ip_addr=208.110.72.10&#39; dspace.log.2018-07-12
1885
</code></pre><ul>
<li>I think the problem is that, despite the bot requesting <code>robots.txt</code>, it almost exlusively requests dynamic pages from <code>/discover</code>:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;Pcore-HTTP&quot; | grep -o -E &quot;GET /(browse|discover|search-filter)&quot; | sort -n | uniq -c | sort -rn
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;Pcore-HTTP&#34; | grep -o -E &#34;GET /(browse|discover|search-filter)&#34; | sort -n | uniq -c | sort -rn
13364 GET /discover
993 GET /search-filter
804 GET /browse
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;Pcore-HTTP&quot; | grep robots
208.110.72.10 - - [12/Jul/2018:00:22:28 +0000] &quot;GET /robots.txt HTTP/1.1&quot; 200 1301 &quot;https://cgspace.cgiar.org/robots.txt&quot; &quot;Pcore-HTTP/v0.44.0&quot;
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;Pcore-HTTP&#34; | grep robots
208.110.72.10 - - [12/Jul/2018:00:22:28 +0000] &#34;GET /robots.txt HTTP/1.1&#34; 200 1301 &#34;https://cgspace.cgiar.org/robots.txt&#34; &#34;Pcore-HTTP/v0.44.0&#34;
</code></pre><ul>
<li>So this bot is just like Baiduspider, and I need to add it to the nginx rate limiting</li>
<li>I&rsquo;ll also add it to Tomcat&rsquo;s Crawler Session Manager Valve to force the re-use of a common Tomcat sesssion for all crawlers just in case</li>
@ -408,7 +408,7 @@ $ csvcut -c 1 &lt; /tmp/affiliations.csv &gt; /tmp/affiliations-1.csv
<ul>
<li>Generate a list of affiliations for Peter and Abenet to go over so we can batch correct them before we deploy the new data visualization dashboard:</li>
</ul>
<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv header;
<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;affiliation&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv header;
COPY 4518
</code></pre><h2 id="2018-07-15">2018-07-15</h2>
<ul>
@ -438,14 +438,14 @@ OAI 2.0 manager action ended. It took 697 seconds.
<li>I need to ask the dspace-tech mailing list if the nightly OAI import catches the case of old items that have had metadata or mappings change</li>
<li>ICARDA sent me a list of the ORCID iDs they have in the MEL system and it looks like almost 150 are new and unique to us!</li>
</ul>
<pre tabindex="0"><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq | wc -l
<pre tabindex="0"><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml | grep -oE &#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39; | sort | uniq | wc -l
1020
$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq | wc -l
$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE &#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39; | sort | uniq | wc -l
1158
</code></pre><ul>
<li>I combined the two lists and regenerated the names for all our the ORCID iDs using my <a href="https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b">resolve-orcids.py</a> script:</li>
</ul>
<pre tabindex="0"><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq &gt; /tmp/2018-07-15-orcid-ids.txt
<pre tabindex="0"><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml MEL\ ORCID.json | grep -oE &#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39; | sort | uniq &gt; /tmp/2018-07-15-orcid-ids.txt
$ ./resolve-orcids.py -i /tmp/2018-07-15-orcid-ids.txt -o /tmp/2018-07-15-resolved-orcids.txt -d
</code></pre><ul>
<li>Then I added the XML formatting for controlled vocabularies, sorted the list with GNU sort in vim via <code>% !sort</code> and then checked the formatting with tidy:</li>
@ -465,16 +465,16 @@ $ ./resolve-orcids.py -i /tmp/2018-07-15-orcid-ids.txt -o /tmp/2018-07-15-resolv
<li>For every day in the past week I only see about 50 to 100 requests per day, but then about nine days ago I see 1500 requsts</li>
<li>In there I see two bots making about 750 requests each, and this one is probably Altmetric:</li>
</ul>
<pre tabindex="0"><code>178.33.237.157 - - [09/Jul/2018:17:00:46 +0000] &quot;GET /oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////100 HTTP/1.1&quot; 200 58653 &quot;-&quot; &quot;Apache-HttpClient/4.5.2 (Java/1.8.0_121)&quot;
178.33.237.157 - - [09/Jul/2018:17:01:11 +0000] &quot;GET /oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////200 HTTP/1.1&quot; 200 67950 &quot;-&quot; &quot;Apache-HttpClient/4.5.2 (Java/1.8.0_121)&quot;
<pre tabindex="0"><code>178.33.237.157 - - [09/Jul/2018:17:00:46 +0000] &#34;GET /oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////100 HTTP/1.1&#34; 200 58653 &#34;-&#34; &#34;Apache-HttpClient/4.5.2 (Java/1.8.0_121)&#34;
178.33.237.157 - - [09/Jul/2018:17:01:11 +0000] &#34;GET /oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////200 HTTP/1.1&#34; 200 67950 &#34;-&#34; &#34;Apache-HttpClient/4.5.2 (Java/1.8.0_121)&#34;
...
178.33.237.157 - - [09/Jul/2018:22:10:39 +0000] &quot;GET /oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////73900 HTTP/1.1&quot; 20 0 25049 &quot;-&quot; &quot;Apache-HttpClient/4.5.2 (Java/1.8.0_121)&quot;
178.33.237.157 - - [09/Jul/2018:22:10:39 +0000] &#34;GET /oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////73900 HTTP/1.1&#34; 20 0 25049 &#34;-&#34; &#34;Apache-HttpClient/4.5.2 (Java/1.8.0_121)&#34;
</code></pre><ul>
<li>So if they are getting 100 records per OAI request it would take them 739 requests</li>
<li>I wonder if I should add this user agent to the Tomcat Crawler Session Manager valve&hellip; does OAI use Tomcat sessions?</li>
<li>Appears not:</li>
</ul>
<pre tabindex="0"><code>$ http --print Hh 'https://cgspace.cgiar.org/oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////100'
<pre tabindex="0"><code>$ http --print Hh &#39;https://cgspace.cgiar.org/oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////100&#39;
GET /oai/request?verb=ListRecords&amp;resumptionToken=oai_dc////100 HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
@ -523,17 +523,17 @@ X-XSS-Protection: 1; mode=block
<li>Still discussing dates with IWMI</li>
<li>I looked in the database to see the breakdown of date formats used in <code>dc.date.issued</code>, ie YYYY, YYYY-MM, or YYYY-MM-DD:</li>
</ul>
<pre tabindex="0"><code>dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=15 and text_value ~ '^[0-9]{4}$';
<pre tabindex="0"><code>dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=15 and text_value ~ &#39;^[0-9]{4}$&#39;;
count
-------
53292
(1 row)
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=15 and text_value ~ '^[0-9]{4}-[0-9]{2}$';
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=15 and text_value ~ &#39;^[0-9]{4}-[0-9]{2}$&#39;;
count
-------
3818
(1 row)
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=15 and text_value ~ '^[0-9]{4}-[0-9]{2}-[0-9]{2}$';
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=15 and text_value ~ &#39;^[0-9]{4}-[0-9]{2}-[0-9]{2}$&#39;;
count
-------
17357