December, 2016
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
/solrso 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
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
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_buffersin PostgreSQL configuration (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-authorityruns 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, andlast_namefields… - 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
updateLogneeds 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)
- Deploy “take task” hack/fix on CGSpace (#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 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_bufferson 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_buffersfor CGSpace’s PostgreSQL configuration the number of connections to the database dropped significantly
- 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.authorfield, and some in others likedc.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_bufferschange from a few days ago really made a big impact:
- 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.logbecause 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’tdspace.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
xzgrepandxzlesswe 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 -Bandionice -c2 -n7to set the CPU scheduling toSCHED_BATCHand 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.txtfile not found error - After applying pull request #291 on DSpace Test I no longer see the error in the logs after the
UpdateSolrStorageReportstask runs - Also, I’m toying with the idea of moving the
tomcat7user’s cron jobs to/etc/cron.dso we can manage them in Ansible - Made a pull request with a template for the cron jobs (#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, 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-servercommand and submit the newsitebndl.zipfile 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
2016-12-18
- Add four new CRP subjects for 2017 and sort the input forms alphabetically (#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)
- 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)
- 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.zipwith 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.accessionedfield - I had to export it from the command line using the
-aflag:
$ [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:
- I will have to check later why the size keeps increasing