<li>Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
<ul>
<li>So far we’ve spent at least fifty hours to process the statistics and statistics-2019 core… wow.</li>
</ul>
</li>
</ul>
<h2id="2020-11-02">2020-11-02</h2>
<ul>
<li>Talk to Moayad and fix a few issues on OpenRXV:
<ul>
<li>Incorrect views and downloads (caused by Elasticsearch’s default result set size of 10)</li>
<li>Invalid share link</li>
<li>Missing “https://” for Handles in the Simple Excel report (caused by using the <code>handle</code> instead of the <code>uri</code>)</li>
<li>Sorting the list of items by views</li>
</ul>
</li>
<li>I resumed the processing of the statistics-2018 Solr core after it spent 20 hours to get to 60%</li>
</ul>
<h2id="2020-11-04">2020-11-04</h2>
<ul>
<li>After 29 hours the statistics-2017 core finished processing so I started the statistics-2016 core on DSpace Test</li>
<li>The statistics-2014 core finished processing after five hours, so I started processing the statistics-2013 core on DSpace Test</li>
<li>Since I was going to restart CGSpace and update the Discovery indexes anyways I decided to check for any straggling upper case AGROVOC entries and lower case them:</li>
</ul>
<pre><code>dspace=# BEGIN;
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE resource_type_id=2 AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
UPDATE 164
dspace=# COMMIT;
</code></pre><ul>
<li>Run system updates on CGSpace (linode18) and reboot it
<ul>
<li>I had to restart Tomcat once after the machine started up to get all Solr statistics cores to load properly</li>
<li>After about ten more hours the rest of the Solr statistics cores finished processing on DSpace Test and I started optimizing them in Solr admin UI</li>
</ul>
<h2id="2020-11-10">2020-11-10</h2>
<ul>
<li>I am noticing that CGSpace doesn’t have any statistics showing for years before 2020, but all cores are loaded successfully in Solr Admin UI… strange
<ul>
<li>I restarted Tomcat and I see in Solr Admin UI that the statistics-2015 core failed to load</li>
<li>Looking in the DSpace log I see:</li>
</ul>
</li>
</ul>
<pre><code>2020-11-10 08:43:59,634 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:43:59,687 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2018
2020-11-10 08:43:59,707 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:44:00,004 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,005 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,005 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,325 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2015
</code></pre><ul>
<li>Seems that the core gets probed twice… perhaps a threading issue?
<ul>
<li>The only thing I can think of is the <code>acceptorThreadCount</code> parameter in Tomcat’s server.xml, which has been set to 2 since 2018-01 (we started sharding the Solr statistics cores in 2019-01 and that’s when this problem arose)</li>
<li>I will try reducing that to 1</li>
<li>Wow, now it’s even worse:</li>
</ul>
</li>
</ul>
<pre><code>2020-11-10 08:51:03,007 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2018
2020-11-10 08:51:03,008 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:51:03,137 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2018
2020-11-10 08:51:03,153 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:51:03,289 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2015
2020-11-10 08:51:03,289 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2010
2020-11-10 08:51:03,475 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2010
2020-11-10 08:51:03,475 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2016
2020-11-10 08:51:03,730 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2016
2020-11-10 08:51:03,731 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2017
2020-11-10 08:51:03,992 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2017
2020-11-10 08:51:03,992 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2011
2020-11-10 08:51:04,178 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2011
2020-11-10 08:51:04,178 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2012
</code></pre><ul>
<li>Could it be because we have two Tomcat connectors?
<ul>
<li>I restarted Tomcat a few more times before all cores loaded, and still there are no stats before 2020-01… hmmmmm</li>
</ul>
</li>
<li>I added a <ahref="https://github.com/ilri/OpenRXV/commit/3816b9b3f3d9182d2ba1a899c1017c5895a59dee">lowercase formatter to OpenRXV</a> so that we can lowercase AGROVOC subjects during harvesting</li>
<li>Atmire responded with a quote for the work to fix the duplicate owningComm, etc in our Solr data
<ul>
<li>I told them to proceed, as it’s within our budget of credits</li>
<li>They will write a processor for DSpace 6 to remove the duplicates</li>
</ul>
</li>
<li>I did some tests to add a usage statistics chart to the item views on DSpace Test
<ul>
<li>It is inspired by Salem’s work on WorldFish’s repository, and it hits the dspace-statistics-api for the current item and displays a graph</li>
<li>I got it working very easily for all-time statistics with Chart.js, but I think I will need to use Highcharts or something else because Chart.js is HTML5 canvas and doesn’t allow theming via CSS (so our Bootstrap brand colors for each theme won’t work)
<ul>
<li>Hmm, Highcharts is not licensed under and open source license so I will not use it</li>
<li>Perhaps I’ll use Chartist with the popover plugin…</li>
<li>I think I’ll pursue this after the DSpace 6 upgrade…</li>
</ul>
</li>
</ul>
<h2id="2020-11-12">2020-11-12</h2>
<ul>
<li>I was looking at Solr again trying to find a way to get community and collection stats by faceting on <code>owningComm</code> and <code>owningColl</code> and it seems to work actually
<ul>
<li>The duplicated values in the multi-value fields don’t seem to affect the counts, as I had thought previously (though we should still get rid of them)</li>
<li>One major difference between the raw numbers I was looking at and Atmire’s numbers is that Atmire’s code filters “Internal” IP addresses…</li>
<li>Also, instead of doing <code>isBot:false</code> I think I should do <code>-isBot:true</code> because it’s not a given that all documents will have this field and have it false, but we can definitely exclude the ones that have it as true</li>
</ul>
</li>
<li>First we get the total number of communities with stats (using calcdistinct):</li>
<li>I was surprised to see 10,000,000 docs with <code>isBot:true</code> when I was testing on DSpace Test…
<ul>
<li>This has got to be a mistake of some kind, as I see 4 million in 2014 that are from <code>dns:localhost.</code>, perhaps that’s when we didn’t have useProxies set up correctly?</li>
<li>I don’t see the same thing on CGSpace… I wonder what happened?</li>
<li>Perhaps they got re-tagged during the DSpace 6 upgrade, somehow during the Solr migration? Hmmmmm. Definitely have to be careful with <code>isBot:true</code> in the future and not automatically purge these!!!</li>
</ul>
</li>
<li>I noticed 120,000+ hits from monit, FeedBurner, and Blackboard Safeassign in 2014, 2015, 2016, 2017, etc…
<ul>
<li>I hadn’t seen monit before, but the others are already in DSpace’s spider agents lists for some time so probably only appear in older stats cores</li>
<li>The issue with purging these using <code>check-spider-hits.sh</code> is that it can’t do case-insensitive regexes and some metacharacters like <code>\s</code> don’t work so I added case-sensitive patterns to a local agents file and purged them with the script</li>
- Error: com.sun.mail.smtp.SMTPSendFailedException: 451 5.7.3 STARTTLS is required to send mail [AM4PR0701CA0003.eurprd07.prod.outlook.com]
</code></pre><ul>
<li>I copied the <code>mail.extraproperties = mail.smtp.starttls.enable=true</code> setting from the old DSpace 5 <code>dspace.cfg</code> and now the emails are working</li>
<li>After the Discovery indexing finished I started processing the Solr stats one core and 2.5 million records at a time:</li>
<li>After about 6,000,000 records I got the same error that I’ve gotten every time I test this migration process:</li>
</ul>
<pre><code>Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
<li>Users are having issues submitting items to CGSpace
<ul>
<li>Looking at the data I see that connections skyrocketed since DSpace 6 upgrade yesterday, and they are all in “waiting for lock” state:</li>
<pre><code>$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1494
</code></pre><ul>
<li>I sent a mail to the dspace-tech mailing list to ask for help…
<ul>
<li>For now I just restarted PostgreSQL and a few users were able to complete submissions…</li>
</ul>
</li>
<li>While processing the statistics-2018 Solr core I got the <em>same</em> memory error that I have gotten every time I processed this core in testing:</li>
</ul>
<pre><code>Exception: Java heap space
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3332)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:124)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:448)
at java.lang.StringBuffer.append(StringBuffer.java:270)
at java.io.StringWriter.write(StringWriter.java:101)
at org.apache.solr.common.util.XML.writeXML(XML.java:133)
at org.apache.solr.client.solrj.util.ClientUtils.writeVal(SourceFile:160)
at org.apache.solr.client.solrj.util.ClientUtils.writeXML(SourceFile:128)
at org.apache.solr.client.solrj.request.UpdateRequest.writeXML(UpdateRequest.java:365)
at org.apache.solr.client.solrj.request.UpdateRequest.getXML(UpdateRequest.java:281)
at org.apache.solr.client.solrj.request.RequestWriter.getContentStream(RequestWriter.java:67)
at org.apache.solr.client.solrj.request.RequestWriter$LazyContentStream.getDelegate(RequestWriter.java:95)
at org.apache.solr.client.solrj.request.RequestWriter$LazyContentStream.getName(RequestWriter.java:105)
at org.apache.solr.client.solrj.impl.HttpSolrServer.createMethod(HttpSolrServer.java:302)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><ul>
<li>I increased the Java heap memory to 4096MB and restarted the processing
<ul>
<li>After a few hours I got the following error, which I have gotten several times over the last few months:</li>
</ul>
</li>
</ul>
<pre><code>Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><h2id="2020-11-17">2020-11-17</h2>
<ul>
<li>Chat with Peter about using some remaining CRP Livestock open access money to fund more work on OpenRXV / AReS
<ul>
<li>I will create GitHub issues for each of the things we talked about and then create ToRs to send to CodeObia for a quote</li>
</ul>
</li>
<li>Continue migrating Solr statistics to DSpace 6 UUID format after the upgrade on Sunday</li>
<li>Regarding the IWMI issue about flagships and strategic priorities we can use CRP Livestock as an example because all their <ahref="https://cgspace.cgiar.org/handle/10568/80102">flagships are mapped to collections</a></li>
