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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-12-02T10:43:00+03:00">Fri Dec 02, 2016</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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<h2 id="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
</ul>
<pre><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail="dc.title", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail="THUMBNAIL", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail="-1", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
</code></pre>
<ul>
<li>I see thousands of them in the logs for the last few months, so it’s not related to the DSpace 5.5 upgrade</li>
<li>I’ve raised a ticket with Atmire to ask</li>
<li>Another worrying error from dspace.log is:</li>
</ul>
<pre><code>org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:789)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:111)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter.doFilter(DSpaceCocoonServletFilter.java:274)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.servlet.multipart.DSpaceMultipartFilter.doFilter(DSpaceMultipartFilter.java:119)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at com.googlecode.psiprobe.Tomcat70AgentValve.invoke(Tomcat70AgentValve.java:44)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at com.atmire.statistics.generator.TopNDSODatasetGenerator.toDatasetQuery(SourceFile:39)
at com.atmire.statistics.display.StatisticsDataVisitsMultidata.createDataset(SourceFile:108)
at org.dspace.statistics.content.StatisticsDisplay.createDataset(SourceFile:384)
at org.dspace.statistics.content.StatisticsDisplay.getDataset(SourceFile:404)
at com.atmire.statistics.mostpopular.JSONStatsMostPopularGenerator.generateJsonData(SourceFile:170)
at com.atmire.statistics.mostpopular.JSONStatsMostPopularGenerator.generate(SourceFile:246)
at com.atmire.app.xmlui.aspect.statistics.JSONStatsMostPopular.generate(JSONStatsMostPopular.java:145)
at sun.reflect.GeneratedMethodAccessor296.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy96.process(Unknown Source)
at org.apache.cocoon.components.treeprocessor.sitemap.ReadNode.invoke(ReadNode.java:94)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelinesNode.invoke(PipelinesNode.java:81)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:239)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:171)
at org.apache.cocoon.components.treeprocessor.TreeProcessor.process(TreeProcessor.java:247)
at org.apache.cocoon.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:117)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelinesNode.invoke(PipelinesNode.java:81)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:239)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:171)
at org.apache.cocoon.components.treeprocessor.TreeProcessor.process(TreeProcessor.java:247)
at org.apache.cocoon.servlet.RequestProcessor.process(RequestProcessor.java:351)
at org.apache.cocoon.servlet.RequestProcessor.service(RequestProcessor.java:169)
at org.apache.cocoon.sitemap.SitemapServlet.service(SitemapServlet.java:84)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:468)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:443)
at org.apache.cocoon.servletservice.spring.ServletFactoryBean$ServiceInterceptor.invoke(ServletFactoryBean.java:264)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy89.service(Unknown Source)
at org.dspace.springmvc.CocoonView.render(CocoonView.java:113)
at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1180)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:950)
... 35 more
</code></pre>
<ul>
<li>The first error I see in dspace.log this morning is:</li>
</ul>
<pre><code>2016-12-02 03:00:46,656 ERROR org.dspace.authority.AuthorityValueFinder @ anonymous::Error while retrieving AuthorityValue from solr:query\colon; id\colon;"b0b541c1-ec15-48bf-9209-6dbe8e338cdc"
org.apache.solr.client.solrj.SolrServerException: Server refused connection at: http://localhost:8081/solr/authority
</code></pre>
<ul>
<li>Looking through DSpace’s solr log I see that about 20 seconds before this, there were a few 30+ KiB solr queries</li>
<li>The last logs here right before Solr became unresponsive (and right after I restarted it five hours later) were:</li>
</ul>
<pre><code>2016-12-02 03:00:42,606 INFO org.apache.solr.core.SolrCore @ [statistics] webapp=/solr path=/select params={q=containerItem:72828+AND+type:0&shards=localhost:8081/solr/statistics-2010,localhost:8081/solr/statistics&fq=-isInternal:true&fq=-(author_mtdt:"CGIAR\+Institutional\+Learning\+and\+Change\+Initiative"++AND+subject_mtdt:"PARTNERSHIPS"+AND+subject_mtdt:"RESEARCH"+AND+subject_mtdt:"AGRICULTURE"+AND+subject_mtdt:"DEVELOPMENT"++AND+iso_mtdt:"en"+)&rows=0&wt=javabin&version=2} hits=0 status=0 QTime=19
2016-12-02 08:28:23,908 INFO org.apache.solr.servlet.SolrDispatchFilter @ SolrDispatchFilter.init()
</code></pre>
<ul>
<li>DSpace’s own Solr logs don’t give IP addresses, so I will have to enable Nginx’s logging of <code>/solr</code> so I can see where this request came from</li>
<li>I enabled logging of <code>/rest/</code> and I think I’ll leave it on for good</li>
<li>Also, the disk is nearly full because of log file issues, so I’m running some compression on DSpace logs</li>
<li>Normally these stay uncompressed for a month just in case we need to look at them, so now I’ve just compressed anything older than 2 weeks so we can get some disk space back</li>
</ul>
<h2 id="2016-12-04">2016-12-04</h2>
<ul>
<li>I got a weird report from the CGSpace checksum checker this morning</li>
<li>It says 732 bitstreams have potential issues, for example:</li>
</ul>
<pre><code>------------------------------------------------
Bitstream Id = 6
Process Start Date = Dec 4, 2016
Process End Date = Dec 4, 2016
Checksum Expected = a1d9eef5e2d85f50f67ce04d0329e96a
Checksum Calculated = a1d9eef5e2d85f50f67ce04d0329e96a
Result = Bitstream marked deleted in bitstream table
-----------------------------------------------
...
------------------------------------------------
Bitstream Id = 77581
Process Start Date = Dec 4, 2016
Process End Date = Dec 4, 2016
Checksum Expected = 9959301aa4ca808d00957dff88214e38
Checksum Calculated =
Result = The bitstream could not be found
-----------------------------------------------
</code></pre>
<ul>
<li>The first one seems ok, but I don’t know what to make of the second one…</li>
<li>I had a look and there is indeed no file with the second checksum in the assetstore (ie, looking in <code>[dspace-dir]/assetstore/99/59/30/...</code>)</li>
<li>For what it’s worth, there is no item on DSpace Test or S3 backups with that checksum either…</li>
<li>In other news, I’m looking at JVM settings from the Solr 4.10.2 release, from <code>bin/solr.in.sh</code>:</li>
</ul>
<pre><code># These GC settings have shown to work well for a number of common Solr workloads
GC_TUNE="-XX:-UseSuperWord \
-XX:NewRatio=3 \
-XX:SurvivorRatio=4 \
-XX:TargetSurvivorRatio=90 \
-XX:MaxTenuringThreshold=8 \
-XX:+UseConcMarkSweepGC \
-XX:+UseParNewGC \
-XX:ConcGCThreads=4 -XX:ParallelGCThreads=4 \
-XX:+CMSScavengeBeforeRemark \
-XX:PretenureSizeThreshold=64m \
-XX:CMSFullGCsBeforeCompaction=1 \
-XX:+UseCMSInitiatingOccupancyOnly \
-XX:CMSInitiatingOccupancyFraction=50 \
-XX:CMSTriggerPermRatio=80 \
-XX:CMSMaxAbortablePrecleanTime=6000 \
-XX:+CMSParallelRemarkEnabled \
-XX:+ParallelRefProcEnabled \
-XX:+AggressiveOpts"
</code></pre>
<ul>
<li>I need to try these because they are recommended by the Solr project itself</li>
<li>Also, as always, I need to read <a href="https://wiki.apache.org/solr/ShawnHeisey">Shawn Heisey’s wiki page on Solr</a></li>
</ul>
<h2 id="2016-12-05">2016-12-05</h2>
<ul>
<li>I did some basic benchmarking on a local DSpace before and after the JVM settings above, but there wasn’t anything amazingly obvious</li>
<li>I want to make the changes on DSpace Test and monitor the JVM heap graphs for a few days to see if they change the JVM GC patterns or anything (munin graphs)</li>
<li>Spin up new CGSpace server on Linode</li>
<li>I did a few traceroutes from Jordan and Kenya and it seems that Linode’s Frankfurt datacenter is a few less hops and perhaps less packet loss than the London one, so I put the new server in Frankfurt</li>
<li>Do initial provisioning</li>
<li>Atmire responded about the MQM warnings in the DSpace logs</li>
<li>Apparently we need to change the batch edit consumers in <code>dspace/config/dspace.cfg</code>:</li>
</ul>
<pre><code>event.consumer.batchedit.filters = Community|Collection+Create
</code></pre>
<ul>
<li>I haven’t tested it yet, but I created a pull request: <a href="https://github.com/ilri/DSpace/pull/289">#289</a></li>
</ul>
<h2 id="2016-12-06">2016-12-06</h2>
<ul>
<li>Some author authority corrections and name standardizations for Peter:</li>
</ul>
<pre><code>dspace=# update metadatavalue set authority='b041f2f4-19e7-4113-b774-0439baabd197', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Mora Benard%';
UPDATE 11
dspace=# update metadatavalue set text_value = 'Hoek, Rein van der', authority='4d6cbce2-6fd5-4b43-9363-58d18e7952c9', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Hoek, R%';
UPDATE 36
dspace=# update metadatavalue set text_value = 'Hoek, Rein van der', authority='4d6cbce2-6fd5-4b43-9363-58d18e7952c9', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like '%an der Hoek%' and text_value !~ '^.*W\.?$';
UPDATE 14
dspace=# update metadatavalue set authority='18349f29-61b1-44d7-ac60-89e55546e812', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Thorne, P%';
UPDATE 42
dspace=# update metadatavalue set authority='0d8369bb-57f7-4b2f-92aa-af820b183aca', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Thornton, P%';
UPDATE 360
dspace=# update metadatavalue set text_value='Grace, Delia', authority='0b4fcbc1-d930-4319-9b4d-ea1553cca70b', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Grace, D%';
UPDATE 561
</code></pre>
<ul>
<li>Pay attention to the regex to prevent false positives in tricky cases with Dutch names!</li>
<li>I will run these updates on DSpace Test and then force a Discovery reindex, and then run them on CGSpace next week</li>
<li>More work on the KM4Dev Journal article</li>
<li>In other news, it seems the batch edit patch is working, there are no more WARN errors in the logs and the batch edit seems to work</li>
<li>I need to check the CGSpace logs to see if there are still errors there, and then deploy/monitor it there</li>
<li>Paola from CCAFS mentioned she also has the “take task” bug on CGSpace</li>
<li>Reading about <a href="https://www.postgresql.org/docs/9.5/static/runtime-config-resource.html"><code>shared_buffers</code> in PostgreSQL configuration</a> (default is 128MB)</li>
<li>Looks like we have ~5GB of memory used by caches on the test server (after OS and JVM heap!), so we might as well bump up the buffers for Postgres</li>
<li>The docs say a good starting point for a dedicated server is 25% of the system RAM, and our server isn’t dedicated (also runs Solr, which can benefit from OS cache) so let’s try 1024MB</li>
<li>In other news, the authority reindexing keeps crashing (I was manually running it after the author updates above):</li>
</ul>
<pre><code>$ time JAVA_OPTS="-Xms768m -Xmx768m -Dfile.encoding=UTF-8" /home/dspacetest.cgiar.org/bin/dspace index-authority
Retrieving all data
Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
Exception: null
java.lang.NullPointerException
at org.dspace.authority.AuthorityValueGenerator.generateRaw(AuthorityValueGenerator.java:82)
at org.dspace.authority.AuthorityValueGenerator.generate(AuthorityValueGenerator.java:39)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.prepareNextValue(DSpaceAuthorityIndexer.java:201)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:132)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:144)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:144)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:159)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:144)
at org.dspace.authority.indexer.DSpaceAuthorityIndexer.hasMore(DSpaceAuthorityIndexer.java:144)
at org.dspace.authority.indexer.AuthorityIndexClient.main(AuthorityIndexClient.java:61)
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:226)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
real 8m39.913s
user 1m54.190s
sys 0m22.647s
</code></pre>
<h2 id="2016-12-07">2016-12-07</h2>
<ul>
<li>For what it’s worth, after running the same SQL updates on my local test server, <code>index-authority</code> runs and completes just fine</li>
<li>I will have to test more</li>
<li>Anyways, I noticed that some of the authority values I set actually have versions of author names we don’t want, ie “Grace, D.”</li>
<li>For example, do a Solr query for “first_name:Grace” and look at the results</li>
<li>Querying that ID shows the fields that need to be changed:</li>
</ul>
<pre><code>{
"responseHeader": {
"status": 0,
"QTime": 1,
"params": {
"q": "id:0b4fcbc1-d930-4319-9b4d-ea1553cca70b",
"indent": "true",
"wt": "json",
"_": "1481102189244"
}
},
"response": {
"numFound": 1,
"start": 0,
"docs": [
{
"id": "0b4fcbc1-d930-4319-9b4d-ea1553cca70b",
"field": "dc_contributor_author",
"value": "Grace, D.",
"deleted": false,
"creation_date": "2016-11-10T15:13:40.318Z",
"last_modified_date": "2016-11-10T15:13:40.318Z",
"authority_type": "person",
"first_name": "D.",
"last_name": "Grace"
}
]
}
}
</code></pre>
<ul>
<li>I think I can just update the <code>value</code>, <code>first_name</code>, and <code>last_name</code> fields…</li>
<li>The update syntax should be something like this, but I’m getting errors from Solr:</li>
</ul>
<pre><code>$ curl 'localhost:8081/solr/authority/update?commit=true&wt=json&indent=true' -H 'Content-type:application/json' -d '[{"id":"1","price":{"set":100}}]'
{
"responseHeader":{
"status":400,
"QTime":0},
"error":{
"msg":"Unexpected character '[' (code 91) in prolog; expected '<'\n at [row,col {unknown-source}]: [1,1]",
"code":400}}
</code></pre>
<ul>
<li>When I try using the XML format I get an error that the <code>updateLog</code> needs to be configured for that core</li>
<li>Maybe I can just remove the authority UUID from the records, run the indexing again so it creates a new one for each name variant, then match them correctly?</li>
</ul>
<pre><code>dspace=# update metadatavalue set authority=null, confidence=-1 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Grace, D%';
UPDATE 561
</code></pre>
<ul>
<li>Then I’ll reindex discovery and authority and see how the authority Solr core looks</li>
<li>After this, now there are authorities for some of the “Grace, D.” and “Grace, Delia” text_values in the database (the first version is actually the same authority that already exists in the core, so it was just added back to some text_values, but the second one is new):</li>
</ul>
<pre><code>$ curl 'localhost:8081/solr/authority/select?q=id%3A18ea1525-2513-430a-8817-a834cd733fbc&wt=json&indent=true'
{
"responseHeader":{
"status":0,
"QTime":0,
"params":{
"q":"id:18ea1525-2513-430a-8817-a834cd733fbc",
"indent":"true",
"wt":"json"}},
"response":{"numFound":1,"start":0,"docs":[
{
"id":"18ea1525-2513-430a-8817-a834cd733fbc",
"field":"dc_contributor_author",
"value":"Grace, Delia",
"deleted":false,
"creation_date":"2016-12-07T10:54:34.356Z",
"last_modified_date":"2016-12-07T10:54:34.356Z",
"authority_type":"person",
"first_name":"Delia",
"last_name":"Grace"}]
}}
</code></pre>
<ul>
<li>So now I could set them all to this ID and the name would be ok, but there has to be a better way!</li>
<li>In this case it seems that since there were also two different IDs in the original database, I just picked the wrong one!</li>
<li>Better to use:</li>
</ul>
<pre><code>dspace#= update metadatavalue set text_value='Grace, Delia', authority='bfa61d7c-7583-4175-991c-2e7315000f0c', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Grace, D%';
</code></pre>
<ul>
<li>This proves that unifying author name varieties in authorities is easy, but fixing the name in the authority is tricky!</li>
<li>Perhaps another way is to just add our own UUID to the authority field for the text_value we like, then re-index authority so they get synced from PostgreSQL to Solr, then set the other text_values to use that authority ID</li>
<li>Deploy MQM WARN fix on CGSpace (<a href="https://github.com/ilri/DSpace/pull/289">#289</a>)</li>
<li>Deploy “take task” hack/fix on CGSpace (<a href="https://github.com/ilri/DSpace/pull/290">#290</a>)</li>
<li>I ran the following author corrections and then reindexed discovery:</li>
</ul>
<pre><code>update metadatavalue set authority='b041f2f4-19e7-4113-b774-0439baabd197', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Mora Benard%';
update metadatavalue set text_value = 'Hoek, Rein van der', authority='4d6cbce2-6fd5-4b43-9363-58d18e7952c9', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Hoek, R%';
update metadatavalue set text_value = 'Hoek, Rein van der', authority='4d6cbce2-6fd5-4b43-9363-58d18e7952c9', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like '%an der Hoek%' and text_value !~ '^.*W\.?$';
update metadatavalue set authority='18349f29-61b1-44d7-ac60-89e55546e812', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Thorne, P%';
update metadatavalue set authority='0d8369bb-57f7-4b2f-92aa-af820b183aca', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Thornton, P%';
update metadatavalue set text_value='Grace, Delia', authority='bfa61d7c-7583-4175-991c-2e7315000f0c', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like 'Grace, D%';
</code></pre>
<h2 id="2016-12-08">2016-12-08</h2>
<ul>
<li>Something weird happened and Peter Thorne’s names all ended up as “Thorne”, I guess because the original authority had that as its name value:</li>
</ul>
<pre><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value like 'Thorne%';
text_value | authority | confidence
------------------+--------------------------------------+------------
Thorne, P.J. | 18349f29-61b1-44d7-ac60-89e55546e812 | 600
Thorne | 18349f29-61b1-44d7-ac60-89e55546e812 | 600
Thorne-Lyman, A. | 0781e13a-1dc8-4e3f-82e8-5c422b44a344 | -1
Thorne, M. D. | 54c52649-cefd-438d-893f-3bcef3702f07 | -1
Thorne, P.J | 18349f29-61b1-44d7-ac60-89e55546e812 | 600
Thorne, P. | 18349f29-61b1-44d7-ac60-89e55546e812 | 600
(6 rows)
</code></pre>
<ul>
<li>I generated a new UUID using <code>uuidgen | tr [A-Z] [a-z]</code> and set it along with correct name variation for all records:</li>
</ul>
<pre><code>dspace=# update metadatavalue set authority='b2f7603d-2fb5-4018-923a-c4ec8d85b3bb', text_value='Thorne, P.J.' where resource_type_id=2 and metadata_field_id=3 and authority='18349f29-61b1-44d7-ac60-89e55546e812';
UPDATE 43
</code></pre>
<ul>
<li>Apparently we also need to normalize Phil Thornton’s names to <code>Thornton, Philip K.</code>:
<br /></li>
</ul>
<pre><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value ~ '^Thornton[,\.]? P.*';
text_value | authority | confidence
---------------------+--------------------------------------+------------
Thornton, P | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton, P K. | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton, P K | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton. P.K. | 3e1e6639-d4fb-449e-9fce-ce06b5b0f702 | -1
Thornton, P K . | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton, P.K. | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton, P.K | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton, Philip K | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton, Philip K. | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
Thornton, P. K. | 0d8369bb-57f7-4b2f-92aa-af820b183aca | 600
(10 rows)
</code></pre>
<ul>
<li>Seems his original authorities are using an incorrect version of the name so I need to generate another UUID and tie it to the correct name, then reindex:</li>
</ul>
<pre><code>dspace=# update metadatavalue set authority='2df8136e-d8f4-4142-b58c-562337cab764', text_value='Thornton, Philip K.', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value ~ '^Thornton[,\.]? P.*';
UPDATE 362
</code></pre>
<ul>
<li>It seems that, when you are messing with authority and author text values in the database, it is better to run authority reindex first (postgres→solr authority core) and then Discovery reindex (postgres→solr Discovery core)</li>
<li>Everything looks ok after authority and discovery reindex</li>
<li>In other news, I think we should really be using more RAM for PostgreSQL’s <code>shared_buffers</code></li>
<li>The <a href="https://www.postgresql.org/docs/9.5/static/runtime-config-resource.html">PostgreSQL documentation</a> recommends using 25% of the system’s RAM on dedicated systems, but we should use a bit less since we also have a massive JVM heap and also benefit from some RAM being used by the OS cache</li>
</ul>
<h2 id="2016-12-09">2016-12-09</h2>
<ul>
<li>More work on finishing rough draft of KM4Dev article</li>
<li>Set PostgreSQL’s <code>shared_buffers</code> on CGSpace to 10% of system RAM (1200MB)</li>
<li>Run the following author corrections on CGSpace:</li>
</ul>
<pre><code>dspace=# update metadatavalue set authority='34df639a-42d8-4867-a3f2-1892075fcb3f', text_value='Thorne, P.J.' where resource_type_id=2 and metadata_field_id=3 and authority='18349f29-61b1-44d7-ac60-89e55546e812' or authority='021cd183-946b-42bb-964e-522ebff02993';
dspace=# update metadatavalue set authority='2df8136e-d8f4-4142-b58c-562337cab764', text_value='Thornton, Philip K.', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value ~ '^Thornton[,\.]? P.*';
</code></pre>
<ul>
<li>The authority IDs were different now than when I was looking a few days ago so I had to adjust them here</li>
</ul>
<h2 id="2016-12-11">2016-12-11</h2>
<ul>
<li>After enabling a sizable <code>shared_buffers</code> for CGSpace’s PostgreSQL configuration the number of connections to the database dropped significantly</li>
</ul>
<p><img src="2016/12/postgres_bgwriter-week.png" alt="postgres_bgwriter-week" />
<img src="2016/12/postgres_connections_ALL-week.png" alt="postgres_connections_ALL-week" /></p>
<ul>
<li>Looking at CIAT records from last week again, they have a lot of double authors like:</li>
</ul>
<pre><code>International Center for Tropical Agriculture::3026b1de-9302-4f3e-85ab-ef48da024eb2::600
International Center for Tropical Agriculture::3026b1de-9302-4f3e-85ab-ef48da024eb2::500
International Center for Tropical Agriculture::3026b1de-9302-4f3e-85ab-ef48da024eb2::0
</code></pre>
<ul>
<li>Some in the same <code>dc.contributor.author</code> field, and some in others like <code>dc.contributor.author[en_US]</code> etc</li>
<li>Removing the duplicates in OpenRefine and uploading a CSV to DSpace says “no changes detected”</li>
<li>Seems like the only way to sortof clean these up would be to start in SQL:</li>
</ul>
<pre><code>dspace=# select distinct text_value, authority, confidence from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value like 'International Center for Tropical Agriculture';
text_value | authority | confidence
-----------------------------------------------+--------------------------------------+------------
International Center for Tropical Agriculture | cc726b78-a2f4-4ee9-af98-855c2ea31c36 | -1
International Center for Tropical Agriculture | | 600
International Center for Tropical Agriculture | 3026b1de-9302-4f3e-85ab-ef48da024eb2 | 500
International Center for Tropical Agriculture | cc726b78-a2f4-4ee9-af98-855c2ea31c36 | 600
International Center for Tropical Agriculture | | -1
International Center for Tropical Agriculture | cc726b78-a2f4-4ee9-af98-855c2ea31c36 | 500
International Center for Tropical Agriculture | 3026b1de-9302-4f3e-85ab-ef48da024eb2 | 600
International Center for Tropical Agriculture | 3026b1de-9302-4f3e-85ab-ef48da024eb2 | -1
International Center for Tropical Agriculture | 3026b1de-9302-4f3e-85ab-ef48da024eb2 | 0
dspace=# update metadatavalue set authority='3026b1de-9302-4f3e-85ab-ef48da024eb2', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value = 'International Center for Tropical Agriculture';
UPDATE 1693
dspace=# update metadatavalue set authority='3026b1de-9302-4f3e-85ab-ef48da024eb2', text_value='International Center for Tropical Agriculture', confidence=600 where resource_type_id=2 and metadata_field_id=3 and text_value like '%CIAT%';
UPDATE 35
</code></pre>
<ul>
<li>Work on article for KM4Dev journal</li>
</ul>
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