+++ 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: <!--more--> ``` 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.*'; ``` - The authority IDs were different now than when I was looking a few days ago so I had to adjust them here ## 2016-12-11 - After enabling a sizable `shared_buffers` for CGSpace's PostgreSQL configuration the number of connections to the database dropped significantly ![postgres_bgwriter-week](/cgspace-notes/2016/12/postgres_bgwriter-week.png) ![postgres_connections_ALL-week](/cgspace-notes/2016/12/postgres_connections_ALL-week.png) - Looking at CIAT records from last week again, they have a lot of double authors like: ``` 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 ``` - Some in the same `dc.contributor.author` field, and some in others like `dc.contributor.author[en_US]` etc - Removing the duplicates in OpenRefine and uploading a CSV to DSpace says "no changes detected" - Seems like the only way to sortof clean these up would be to start in SQL: ``` 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 ``` - Work on article for KM4Dev journal ## 2016-12-13 - Checking in on CGSpace postgres stats again, looks like the `shared_buffers` change from a few days ago really made a big impact: ![postgres_bgwriter-week](/cgspace-notes/2016/12/postgres_bgwriter-week-2016-12-13.png) ![postgres_connections_ALL-week](/cgspace-notes/2016/12/postgres_connections_ALL-week-2016-12-13.png) - Looking at logs, it seems we need to evaluate which logs we keep and for how long - Basically the only ones we *need* are `dspace.log` because those are used for legacy statistics (need to keep for 1 month) - Other logs will be an issue because they don't have date stamps - I will add date stamps to the logs we're storing from the tomcat7 user's cron jobs at least, using: `$(date --iso-8601)` - Would probably be better to make custom logrotate files for them in the future - Clean up some unneeded log files from 2014 (they weren't large, just don't need them) - So basically, new cron jobs for logs should look something like this: - Find any file named `*.log*` that isn't `dspace.log*`, isn't already zipped, and is older than one day, and zip it: ``` # find /home/dspacetest.cgiar.org/log -regextype posix-extended -iregex ".*\.log.*" ! -iregex ".*dspace\.log.*" ! -iregex ".*\.(gz|lrz|lzo|xz)" ! -newermt "Yesterday" -exec schedtool -B -e ionice -c2 -n7 xz {} \; ``` - Since there is `xzgrep` and `xzless` we can actually just zip them after one day, why not?! - We can keep the zipped ones for two weeks just in case we need to look for errors, etc, and delete them after that - I use `schedtool -B` and `ionice -c2 -n7` to set the CPU scheduling to `SCHED_BATCH` and the IO to best effort which should, in theory, impact important system processes like Tomcat and PostgreSQL less - When the tasks are running you can see that the policies do apply: ``` $ schedtool $(ps aux | grep "xz /home" | grep -v grep | awk '{print $2}') && ionice -p $(ps aux | grep "xz /home" | grep -v grep | awk '{print $2}') PID 17049: PRIO 0, POLICY B: SCHED_BATCH , NICE 0, AFFINITY 0xf best-effort: prio 7 ``` - All in all this should free up a few gigs (we were at 9.3GB free when I started) - Next thing to look at is whether we need Tomcat's access logs - I just looked and it seems that we saved 10GB by zipping these logs - Some users pointed out issues with the "most popular" stats on a community or collection - This error appears in the logs when you try to view them: ``` 2016-12-13 21:17:37,486 ERROR org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error Occurred Processing Request! 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:650) at javax.servlet.http.HttpServlet.service(HttpServlet.java:731) 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.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) 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:221) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625) at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) 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.NativeMethodAccessorImpl.invoke0(Native Method) ``` - It happens on development and production, so I will have to ask Atmire - Most likely an issue with installation/configuration ## 2016-12-14 - Atmire sent a quick fix for the `last-update.txt` file not found error - After applying pull request [#291](https://github.com/ilri/DSpace/pull/291) on DSpace Test I no longer see the error in the logs after the `UpdateSolrStorageReports` task runs - Also, I'm toying with the idea of moving the `tomcat7` user's cron jobs to `/etc/cron.d` so we can manage them in Ansible - Made a pull request with a template for the cron jobs ([#75](https://github.com/ilri/rmg-ansible-public/pull/75)) - Testing SMTP from the new CGSpace server and it's not working, I'll have to tell James ## 2016-12-15 - Start planning for server migration this weekend, letting users know - I am trying to figure out what the process is to [update the server's IP in the Handle system](http://handle.net/hnr_support.html), and emailing the hdladmin account bounces(!) - I will contact the Jane Euler directly as I know I've corresponded with her in the past - She said that I should indeed just re-run the `[dspace]/bin/dspace make-handle-server` command and submit the new `sitebndl.zip` file to the CNRI website - Also I was troubleshooting some workflow issues from Bizuwork - I re-created the same scenario by adding a non-admin account and submitting an item, but I was able to successfully approve and commit it - So it turns out it's not a bug, it's just that Peter was added as a reviewer/admin AFTER the items were submitted - This is how DSpace works, and I need to ask if there is a way to override someone's submission, as the other reviewer seems to not be paying attention, or has perhaps taken the item from the task pool? - Run a batch edit to add "RANGELANDS" ILRI subject to all items containing the word "RANGELANDS" in their metadata for Peter Ballantyne ![Select all items with "rangelands" in metadata](/cgspace-notes/2016/12/batch-edit1.png) ![Add RANGELANDS ILRI subject](/cgspace-notes/2016/12/batch-edit2.png) ## 2016-12-18 - Add four new CRP subjects for 2017 and sort the input forms alphabetically ([#294](https://github.com/ilri/DSpace/pull/294)) - Test the SMTP on the new server and it's working - Last week, when we asked CGNET to update the DNS records this weekend, they misunderstood and did it immediately - We quickly told them to undo it, but I just realized they didn't undo the IPv6 AAAA record! - None of our users in African institutes will have IPv6, but some Europeans might, so I need to check if any submissions have been added since then - Update some names and authorities in the database: ``` dspace=# update metadatavalue set authority='5ff35043-942e-4d0a-b377-4daed6e3c1a3', confidence=600, text_value='Duncan, Alan' where resource_type_id=2 and metadata_field_id=3 and text_value ~ '^.*Duncan,? A.*'; UPDATE 204 dspace=# update metadatavalue set authority='46804b53-ea30-4a85-9ccf-b79a35816fa9', confidence=600, text_value='Mekonnen, Kindu' where resource_type_id=2 and metadata_field_id=3 and text_value like '%Mekonnen, K%'; UPDATE 89 dspace=# update metadatavalue set authority='f840da02-26e7-4a74-b7ba-3e2b723f3684', confidence=600, text_value='Lukuyu, Ben A.' where resource_type_id=2 and metadata_field_id=3 and text_value like '%Lukuyu, B%'; UPDATE 140 ``` - Generated a new UUID for Ben using `uuidgen | tr [A-Z] [a-z]` as the one in Solr had his ORCID but the name format was incorrect - In theory DSpace should be able to check names from ORCID and update the records in the database, but I find that this doesn't work (see Jira bug [DS-3302](https://jira.duraspace.org/browse/DS-3302)) - I need to run these updates along with the other one for CIAT that I found last week - Enable OCSP stapling for hosts >= Ubuntu 16.04 in our Ansible playbooks ([#76](https://github.com/ilri/rmg-ansible-public/pull/76)) - Working for DSpace Test on the second response: ``` $ openssl s_client -connect dspacetest.cgiar.org:443 -servername dspacetest.cgiar.org -tls1_2 -tlsextdebug -status ... OCSP response: no response sent $ openssl s_client -connect dspacetest.cgiar.org:443 -servername dspacetest.cgiar.org -tls1_2 -tlsextdebug -status ... OCSP Response Data: ... Cert Status: good ``` - Migrate CGSpace to new server, roughly following these steps: - On old server: ``` # service tomcat7 stop # /home/backup/scripts/postgres_backup.sh ``` - On new server: ``` # systemctl stop tomcat7 # rsync -4 -av --delete 178.79.187.182:/home/cgspace.cgiar.org/assetstore/ /home/cgspace.cgiar.org/assetstore/ # rsync -4 -av --delete 178.79.187.182:/home/backup/ /home/backup/ # rsync -4 -av --delete 178.79.187.182:/home/cgspace.cgiar.org/solr/ /home/cgspace.cgiar.org/solr # su - postgres $ dropdb cgspace $ createdb -O cgspace --encoding=UNICODE cgspace $ psql cgspace -c 'alter user cgspace createuser;' $ pg_restore -O -U cgspace -d cgspace -W -h localhost /home/backup/postgres/cgspace_2016-12-18.backup $ psql cgspace -c 'alter user cgspace nocreateuser;' $ psql -U cgspace -f ~tomcat7/src/git/DSpace/dspace/etc/postgres/update-sequences.sql cgspace -h localhost $ vacuumdb cgspace $ psql cgspace postgres=# \i /tmp/author-authority-updates-2016-12-11.sql postgres=# \q $ exit # chown -R tomcat7:tomcat7 /home/cgspace.cgiar.org # rsync -4 -av 178.79.187.182:/home/cgspace.cgiar.org/log/*.dat /home/cgspace.cgiar.org/log/ # rsync -4 -av 178.79.187.182:/home/cgspace.cgiar.org/log/dspace.log.2016-1[12]* /home/cgspace.cgiar.org/log/ # su - tomcat7 $ cd src/git/DSpace/dspace/target/dspace-installer $ ant update clean_backups $ exit # systemctl start tomcat7 ``` - It took about twenty minutes and afterwards I had to check a few things, like: - check and enable systemd timer for let's encrypt - enable root cron jobs - disable root cron jobs on old server after! - enable tomcat7 cron jobs - disable tomcat7 cron jobs on old server after! - regenerate `sitebndl.zip` with new IP for handle server and submit it to Handle.net ## 2016-12-22 - Abenet wanted a CSV of the IITA community, but the web export doesn't include the `dc.date.accessioned` field - I had to export it from the command line using the `-a` flag: ``` $ [dspace]/bin/dspace metadata-export -a -f /tmp/iita.csv -i 10568/68616 ``` ## 2016-12-28 - We've been getting two alerts per day about CPU usage on the new server from Linode - These are caused by the batch jobs for Solr etc that run in the early morning hours - The Linode default is to alert at 90% CPU usage for two hours, but I see the old server was at 150%, so maybe we just need to adjust it - Speaking of the old server (linode01), I think we can decommission it now - I checked the S3 logs on the new server (linode18) to make sure the backups have been running and everything looks good - In other news, I was looking at the Munin graphs for PostgreSQL on the new server and it looks slightly worrying: ![munin postgres stats](/cgspace-notes/2016/12/postgres_size_ALL-week.png) - I will have to check later why the size keeps increasing