+++ date = "2016-12-02T10:43:00+03:00" author = "Alan Orth" title = "December, 2016" tags = ["Notes"] +++ ## 2016-12-02 - CGSpace was down for five hours in the morning while I was sleeping - While looking in the logs for errors, I see tons of warnings about Atmire MQM: ``` 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") ``` - I see thousands of them in the logs for the last few months, so it's not related to the DSpace 5.5 upgrade - I've raised a ticket with Atmire to ask - Another worrying error from dspace.log is: ``` 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 ``` - The first error I see in dspace.log this morning is: ``` 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 ``` - Looking through DSpace's solr log I see that about 20 seconds before this, there were a few 30+ KiB solr queries - The last logs here right before Solr became unresponsive (and right after I restarted it five hours later) were: ``` 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() ``` - DSpace's own Solr logs don't give IP addresses, so I will have to enable Nginx's logging of `/solr` so I can see where this request came from - I enabled logging of `/rest/` and I think I'll leave it on for good - Also, the disk is nearly full because of log file issues, so I'm running some compression on DSpace logs - 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 ## 2016-12-04 - I got a weird report from the CGSpace checksum checker this morning - It says 732 bitstreams have potential issues, for example: ``` ------------------------------------------------ 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 ----------------------------------------------- ``` - The first one seems ok, but I don't know what to make of the second one... - I had a look and there is indeed no file with the second checksum in the assetstore (ie, looking in `[dspace-dir]/assetstore/99/59/30/...`) - For what it's worth, there is no item on DSpace Test or S3 backups with that checksum either... - In other news, I'm looking at JVM settings from the Solr 4.10.2 release, from `bin/solr.in.sh`: ``` # 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" ``` - I need to try these because they are recommended by the Solr project itself - Also, as always, I need to read [Shawn Heisey's wiki page on Solr](https://wiki.apache.org/solr/ShawnHeisey) ## 2016-12-05 - I did some basic benchmarking on a local DSpace before and after the JVM settings above, but there wasn't anything amazingly obvious - 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) - Spin up new CGSpace server on Linode - 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 - Do initial provisioning - Atmire responded about the MQM warnings in the DSpace logs - Apparently we need to change the batch edit consumers in `dspace/config/dspace.cfg`: ``` event.consumer.batchedit.filters = Community|Collection+Create ``` - I haven't tested it yet, but I created a pull request: [#289](https://github.com/ilri/DSpace/pull/289) ## 2016-12-06 - Some author authority corrections and name standardizations for Peter: ``` 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 ``` - Pay attention to the regex to prevent false positives in tricky cases with Dutch names! - I will run these updates on DSpace Test and then force a Discovery reindex, and then run them on CGSpace next week - More work on the KM4Dev Journal article - 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 - I need to check the CGSpace logs to see if there are still errors there, and then deploy/monitor it there - Paola from CCAFS mentioned she also has the "take task" bug on CGSpace - Reading about [`shared_buffers` in PostgreSQL configuration](https://www.postgresql.org/docs/9.5/static/runtime-config-resource.html) (default is 128MB) - 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 - 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 - In other news, the authority reindexing keeps crashing (I was manually running it after the author updates above): ``` $ 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 ``` ## 2016-12-07 - For what it's worth, after running the same SQL updates on my local test server, `index-authority` runs and completes just fine - I will have to test more - Anyways, I noticed that some of the authority values I set actually have versions of author names we don't want, ie "Grace, D." - For example, do a Solr query for "first_name:Grace" and look at the results - Querying that ID shows the fields that need to be changed: ``` { "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" } ] } } ``` - I think I can just update the `value`, `first_name`, and `last_name` fields... - The update syntax should be something like this, but I'm getting errors from Solr: ``` $ 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}} ``` - When I try using the XML format I get an error that the `updateLog` needs to be configured for that core - 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? ``` 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 ``` - Then I'll reindex discovery and authority and see how the authority Solr core looks - 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): ``` $ 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"}] }} ``` - So now I could set them all to this ID and the name would be ok, but there has to be a better way! - In this case it seems that since there were also two different IDs in the original database, I just picked the wrong one! - Better to use: ``` 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%'; ``` - This proves that unifying author name varieties in authorities is easy, but fixing the name in the authority is tricky! - 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 - Deploy MQM WARN fix on CGSpace ([#289](https://github.com/ilri/DSpace/pull/289)) - Deploy "take task" hack/fix on CGSpace ([#290](https://github.com/ilri/DSpace/pull/290)) - I ran the following author corrections and then reindexed discovery: ``` 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%'; ``` ## 2016-12-08 - 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: ``` 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) ``` - I generated a new UUID using `uuidgen | tr [A-Z] [a-z]` and set it along with correct name variation for all records: ``` 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 ``` - Apparently we also need to normalize Phil Thornton's names to `Thornton, Philip K.`: ``` 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) ``` - 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: ``` 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 ``` - 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) - Everything looks ok after authority and discovery reindex - In other news, I think we should really be using more RAM for PostgreSQL's `shared_buffers` - The [PostgreSQL documentation](https://www.postgresql.org/docs/9.5/static/runtime-config-resource.html) 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 ## 2016-12-09 - More work on finishing rough draft of KM4Dev article - Set PostgreSQL's `shared_buffers` on CGSpace to 10% of system RAM (1200MB) - Run the following author corrections on CGSpace: ``` 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.*'; ```