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Updated tsv metadata blocks for Beta #485

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eaquigley opened this issue Jul 9, 2014 · 7 comments
Closed

Updated tsv metadata blocks for Beta #485

eaquigley opened this issue Jul 9, 2014 · 7 comments
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Type: Feature a feature request

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@eaquigley
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Author Name: Eleni Castro (@posixeleni)
Original Redmine Issue: 3900, https://redmine.hmdc.harvard.edu/issues/3900
Original Date: 2014-04-29
Original Assignee: Kevin Condon


Updated the following TSV metadata blocks for Beta, which will need schema.xml to be run and then QA on the following changes:

  • General:
    ** changed descriptions to be more uniform definitions rather than instructions including:
    *** updated Subject to have a more helpful definition for users (Issue Improve reporting of ingest failures #3769)
    *** updated Contact to say that email will not show.
    ** moved Data Sources into Social Science block
    ** added watermark for Contributor Name
  • Social Science:
    ** created compound fields for "Time Period Covered" and "Date of Collection" also added watermarks YYYY-MM-DD for Start and End
    ** made Contributor Name and Contributor Type Facetable and Advance Searchable (boolean TRUE)
    ** removed Contributor Logo URL and Contributor URL (based on Issue invalid schema and metadataNamespace fields in OAI-PMH ListMetadataFormats response #3621)
  • Astrophysics (based on Issue tabular mapping: display join column details for user #3494)
    ** removed compound fields for: Coverage, and Redshift.
    ** Made new compounds for fields that would be treated as ranges (dates, units).
    *** coverage.Spectral.Wavelength
    *** coverage.Temporal
    *** coverage.RedshiftValue
    ** For field name disambiguation I changed the field names (field titles remain the same):
    *** astroType, astroFacility, astroInstrument

For QA: I'm assuming they will firstly need to confirm that the fields are there and working as designed but for astro especially due to the special ingest feature we have for FITS will need to test with actual data to make sure it works ok. I think it would be good to have Gus or some other astro people to look these over to make sure the data is displaying as expected.


Related issue(s): #72, #368, #495
Redmine related issue(s): 3480, 3783, 3910


@eaquigley
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Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-04-30T14:38:06Z


It sounds like Eleni might need to fill in more information for coverage.Spectral.Wavelength, for example, which doesn't have a fieldType: https://github.com/IQSS/dataverse/blob/2948e6710b2c9a9dcae216bdcb0d9f1798f09a60/scripts/api/data/metadatablocks/astrophysics.tsv

In code I've written, I call anything without a fieldType an "odd" field and just make it a text_en field:

So I'd really appreciate it if fieldType is always filled in. We should probably put a check in parseDatasetField ( dsf.setFieldType(values[5]) ) for this:

. That check should also be aware of possible field types... the enum idea in #3783.

@eaquigley
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Original Redmine Comment
Author Name: Eleni Castro (@posixeleni)
Original Date: 2014-04-30T16:58:52Z


Fixed missing FieldTypes and missing metadatablock_id. Sending back to Phil to run schema.xml.

@eaquigley
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Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-04-30T17:34:13Z


Eleni Castro wrote:

Fixed missing FieldTypes and missing metadatablock_id. Sending back to Phil to run schema.xml.

I can't re-generate a schema.xml because loading of the metablocks is throwing exceptions.

I'm passing this to Gustavo since he works on all the code to load up metadata blocks from tsv.

To give some more detail, I pulled in this commit...

Fixed missing field types and metadatablock_id · e15a9bd · IQSS/dataverse - e15a9bd

... and tried running scripts/api/datasetfields.sh

It failed with exceptions in DatasetFieldServiceApi.java. The line numbers in the exceptions below correspond too this version of the file:

https://github.com/IQSS/dataverse/blob/e15a9bdcb3b1c2e6c945188929f1e88d9a42d3c2/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java

File parsing completed:

citation MetadataBlock added.
title DatasetField added.
author DatasetField added.
authorName DatasetField added.
authorAffiliation DatasetField added.
distributorContact DatasetField added.
description DatasetField added.
keyword DatasetField added.
subject DatasetField added.
notesText DatasetField added.
otherId DatasetField added.
otherIdValue DatasetField added.
otherIdAgency DatasetField added.
publication DatasetField added.
publicationCitation DatasetField added.
publicationIDType DatasetField added.
publicationIDNumber DatasetField added.
publicationURL DatasetField added.
contributor DatasetField added.
contributorType DatasetField added.
contributorName DatasetField added.
contributorAffiliation DatasetField added.
contributorAbbreviation DatasetField added.
productionDate DatasetField added.
productionPlace DatasetField added.
grantNumber DatasetField added.
grantNumberValue DatasetField added.
grantNumberAgency DatasetField added.
depositor DatasetField added.
dateOfDeposit DatasetField added.
relatedMaterial DatasetField added.
relatedDatasets DatasetField added.
otherReferences DatasetField added.
Arts and Humanities Controlled Vocabulary added.
Astronomy and Astrophysics Controlled Vocabulary added.
Business and Management Controlled Vocabulary added.
Chemistry Controlled Vocabulary added.
Earth and Environmental Sciences Controlled Vocabulary added.
Engineering Controlled Vocabulary added.
Medicine, Health & Life Sciences Controlled Vocabulary added.
Computer and Information Science Controlled Vocabulary added.
Law Controlled Vocabulary added.
Mathematical Sciences Controlled Vocabulary added.
Physics Controlled Vocabulary added.
Social Sciences Controlled Vocabulary added.
Other Controlled Vocabulary added.
ark Controlled Vocabulary added.
arXiv Controlled Vocabulary added.
bibcode Controlled Vocabulary added.
doi Controlled Vocabulary added.
ean13 Controlled Vocabulary added.
eissn Controlled Vocabulary added.
handle Controlled Vocabulary added.
isbn Controlled Vocabulary added.
issn Controlled Vocabulary added.
istc Controlled Vocabulary added.
lissn Controlled Vocabulary added.
lsid Controlled Vocabulary added.
pmid Controlled Vocabulary added.
pmcid Controlled Vocabulary added.
purl Controlled Vocabulary added.
upc Controlled Vocabulary added.
url Controlled Vocabulary added.
urn Controlled Vocabulary added.
Data Collector Controlled Vocabulary added.
Data Manager Controlled Vocabulary added.
Distributor Controlled Vocabulary added.
Editor Controlled Vocabulary added.
Funder Controlled Vocabulary added.
Hosting Institution Controlled Vocabulary added.
Producer Controlled Vocabulary added.
Project Leader Controlled Vocabulary added.
Project Manager Controlled Vocabulary added.
Project Member Controlled Vocabulary added.
Related Person Controlled Vocabulary added.
Researcher Controlled Vocabulary added.
Research Group Controlled Vocabulary added.
Rights Holder Controlled Vocabulary added.
Sponsor Controlled Vocabulary added.
Supervisor Controlled Vocabulary added.
Work Package Leader Controlled Vocabulary added.
Other Controlled Vocabulary added.
File parsing completed:

socialscience MetadataBlock added.
topicClassification DatasetField added.
topicClassValue DatasetField added.
topicClassVocab DatasetField added.
topicClassVocabURI DatasetField added.
software DatasetField added.
softwareName DatasetField added.
softwareVersion DatasetField added.
series DatasetField added.
seriesName DatasetField added.
seriesInformation DatasetField added.
timePeriodCovered DatasetField added.
timePeriodCoveredStart DatasetField added.
timePeriodCoveredEnd DatasetField added.
dateOfCollection DatasetField added.
dateOfCollectionStart DatasetField added.
dateOfCollectionEnd DatasetField added.
country DatasetField added.
geographicCoverage DatasetField added.
geographicUnit DatasetField added.
geographicBoundingBox DatasetField added.
westLongitude DatasetField added.
eastLongitude DatasetField added.
northLongitude DatasetField added.
southLongitude DatasetField added.
unitOfAnalysis DatasetField added.
universe DatasetField added.
kindOfData DatasetField added.
timeMethod DatasetField added.
collectorTraining DatasetField added.
frequencyOfDataCollection DatasetField added.
samplingProcedure DatasetField added.
sampleFrame DatasetField added.
targetSampleSize DatasetField added.
deviationsFromSampleDesign DatasetField added.
collectionMode DatasetField added.
researchInstrument DatasetField added.
dataSources DatasetField added.
originOfSources DatasetField added.
characteristicOfSources DatasetField added.
accessToSources DatasetField added.
dataCollectionSituation DatasetField added.
actionsToMinimizeLoss DatasetField added.
controlOperations DatasetField added.
weighting DatasetField added.
cleaningOperations DatasetField added.
datasetLevelErrorNotes DatasetField added.
responseRate DatasetField added.
samplingErrorEstimates DatasetField added.
otherDataAppraisal DatasetField added.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>GlassFish Server Open Source Edition  4.0  - Error report</title><style type="text/css"><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - Internal Server Error</h1><hr/><p><b>type</b> Exception report</p><p><b>message</b>Internal Server Error</p><p><b>description</b>The server encountered an internal error that prevented it from fulfilling this request.</p><p><b>exception</b> ```javax.servlet.ServletException: javax.ejb.EJBException
```</p><p><b>root cause</b> ```javax.ejb.EJBException
```</p><p><b>root cause</b> ```javax.persistence.NoResultException: getSingleResult&#40;&#41; did not retrieve any entities.
```</p><p><b>note</b> <u>The full stack traces of the exception and its root causes are available in the GlassFish Server Open Source Edition  4.0  logs.</u></p><hr/><h3>GlassFish Server Open Source Edition  4.0 </h3></body></html>File parsing completed:

biomedical MetadataBlock added.
studyDesignType DatasetField added.
studyFactorType DatasetField added.
studyAssayMeasurementType DatasetField added.
studyAssayOrganism DatasetField added.
studyAssayCellType DatasetField added.
Case Control Controlled Vocabulary added.
Cross Sectional Controlled Vocabulary added.
Not Specified Controlled Vocabulary added.
Parallel Group Design Controlled Vocabulary added.
Perturbation Design Controlled Vocabulary added.
Technological Design Controlled Vocabulary added.
Age Controlled Vocabulary added.
Biomarkers Controlled Vocabulary added.
Developmental Stage Controlled Vocabulary added.
Cell Surface Markers Controlled Vocabulary added.
Cell Type/Cell Line Controlled Vocabulary added.
Disease State Controlled Vocabulary added.
Extract Molecule Controlled Vocabulary added.
Genetic Characteristics Controlled Vocabulary added.
Immunoprecipitation Antibody Controlled Vocabulary added.
Organism Controlled Vocabulary added.
Other Controlled Vocabulary added.
Passages Controlled Vocabulary added.
Platform Controlled Vocabulary added.
Sex Controlled Vocabulary added.
Strain Controlled Vocabulary added.
Time Point Controlled Vocabulary added.
Tissue Type Controlled Vocabulary added.
Treatment Compound Controlled Vocabulary added.
Treatment Type Controlled Vocabulary added.
DNA Methylation Profiling (Bisulfite-Seq) Controlled Vocabulary added.
DNA Methylation Profiling (MeDIP-Seq) Controlled Vocabulary added.
Histone Modification (ChIP-Seq) Controlled Vocabulary added.
Protein-RNA Binding (RIP-Seq) Controlled Vocabulary added.
Transcription Factor Binding (ChIP-Seq) Controlled Vocabulary added.
Transcription Profiling (Microarray) Controlled Vocabulary added.
Transcription Profiling (RNA-Seq) Controlled Vocabulary added.
TRAP Translational Profiling Controlled Vocabulary added.
Danio rerio Controlled Vocabulary added.
Homo sapiens Controlled Vocabulary added.
Mus musculus Controlled Vocabulary added.
Rattus norvegicus Controlled Vocabulary added.

Exceptions from server.log:

[2014-04-30T13:18:48.460-0400] [glassfish 4.0] [WARNING] [] [javax.enterprise.system.container.ejb.com.sun.ejb.containers] [tid: _ThreadID=19 _ThreadName=http-listener-1(2)] [timeMillis: 1398878328460] [levelValue: 900] [[

javax.ejb.EJBException
        at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:748)
        at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:698)
        at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:503)
        at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4475)
        at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2009)
        at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:1979)
        at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
        at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
        at com.sun.proxy.$Proxy194.findByName(Unknown Source)
        at edu.harvard.iq.dataverse.__EJB31_Generated__DatasetFieldServiceBean__Intf____Bean__.findByName(Unknown Source)
        at edu.harvard.iq.dataverse.api.DatasetFieldServiceApi.parseControlledVocabulary(DatasetFieldServiceApi.java:231)
        at edu.harvard.iq.dataverse.api.DatasetFieldServiceApi.loadDatasetFields(DatasetFieldServiceApi.java:172)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:125)
        at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:195)
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:91)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:346)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:341)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:101)
        at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:224)
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
        at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
        at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:198)
        at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:946)
        at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:323)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:372)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:335)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:218)
        at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:253)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
        at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
        at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
        at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
        at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:357)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
        at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
        at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:191)
        at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:168)
        at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
        at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
        at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
        at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
        at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
        at java.lang.Thread.run(Thread.java:744)
Caused by: javax.persistence.NoResultException: getSingleResult() did not retrieve any entities.
        at org.eclipse.persistence.internal.jpa.QueryImpl.throwNoResultException(QueryImpl.java:971)
        at org.eclipse.persistence.internal.jpa.QueryImpl.getSingleResult(QueryImpl.java:521)
        at org.eclipse.persistence.internal.jpa.EJBQueryImpl.getSingleResult(EJBQueryImpl.java:400)
        at edu.harvard.iq.dataverse.DatasetFieldServiceBean.findByName(DatasetFieldServiceBean.java:52)
        at sun.reflect.GeneratedMethodAccessor104.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
        at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
        at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4695)
        at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:630)
        at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
        at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
        at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
        at sun.reflect.GeneratedMethodAccessor92.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
        at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
        at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
        at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
        at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
        at sun.reflect.GeneratedMethodAccessor94.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
        at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
        at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
        at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4667)
        at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4655)
        at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
        ... 61 more
]]

[2014-04-30T13:18:48.464-0400] [glassfish 4.0] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=19 _ThreadName=http-listener-1(2)] [timeMillis: 1398878328464] [levelValue: 900] [[
  StandardWrapperValve[edu.harvard.iq.dataverse.api.ApiConfiguration]: Servlet.service() for servlet edu.harvard.iq.dataverse.api.ApiConfiguration threw exception
javax.persistence.NoResultException: getSingleResult() did not retrieve any entities.
        at org.eclipse.persistence.internal.jpa.QueryImpl.throwNoResultException(QueryImpl.java:971)
        at org.eclipse.persistence.internal.jpa.QueryImpl.getSingleResult(QueryImpl.java:521)
        at org.eclipse.persistence.internal.jpa.EJBQueryImpl.getSingleResult(EJBQueryImpl.java:400)
        at edu.harvard.iq.dataverse.DatasetFieldServiceBean.findByName(DatasetFieldServiceBean.java:52)
        at sun.reflect.GeneratedMethodAccessor104.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
        at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
        at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4695)
        at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:630)
        at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
        at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
        at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
        at sun.reflect.GeneratedMethodAccessor92.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
        at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
        at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:582)
        at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
        at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
        at sun.reflect.GeneratedMethodAccessor94.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
        at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
        at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
        at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4667)
        at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4655)
        at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
        at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
        at com.sun.proxy.$Proxy194.findByName(Unknown Source)
        at edu.harvard.iq.dataverse.__EJB31_Generated__DatasetFieldServiceBean__Intf____Bean__.findByName(Unknown Source)
        at edu.harvard.iq.dataverse.api.DatasetFieldServiceApi.parseControlledVocabulary(DatasetFieldServiceApi.java:231)
        at edu.harvard.iq.dataverse.api.DatasetFieldServiceApi.loadDatasetFields(DatasetFieldServiceApi.java:172)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:125)
        at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:195)
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:91)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:346)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:341)
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:101)
        at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:224)
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
        at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
        at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:198)
        at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:946)
        at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:323)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:372)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:335)
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:218)
        at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:253)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
        at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
        at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
        at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
        at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:357)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
        at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
        at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:191)
        at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:168)
        at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
        at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
        at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
        at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
        at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
        at java.lang.Thread.run(Thread.java:744)
]]

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Original Redmine Comment
Author Name: Eleni Castro (@posixeleni)
Original Date: 2014-04-30T22:00:29Z


Found issue that under #controlledvocabulary in astrophysics.tsv the DatasetFieldValue did not match any of the actual dataset field names. Changed "type" to "astroType" and committed changes in git. Also removed #controlledvocabulary row in social_science.tsv since it is currently not being used for this block. Ready for Phil to try again! Fingers crossed.

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Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-05-01T15:31:56Z


I'm not longer seeing exceptions when importing the TSVs. I did a little sanity checking by creating a dataset and as long as you have the new Solr schema.xml in this commit, I don't expect anyone to have any problems:

bring Solr schema.xml up to date with bb178ce #3900 · 2ce1c4f · IQSS/dataverse - 2ce1c4f

Obviously, if anyone does see problems related to indexing, please pass this ticket to me.

Please note that I recently ( https://redmine.hmdc.harvard.edu/issues/3783#note-10 ) learned about that "int" and "float" are being added to the Google Spreadsheet, but I have not yet changed any of the logic to accommodate this. That is to say, anything marked as "int" or "float" in the Google Speadsheet will be indexed as "text_en" (English text) in Solr. Some day, I'd like to actually index these properly as ints and floats in Solr so we can do range queries, as mentioned (sort of) in #3816 and #3478. We could probably use help from Gus or other astro folks on what the UI should look like (if someone could make a separate ticket for this, that would be great. For now let's use this Google Doc: https://docs.google.com/a/harvard.edu/document/d/19DB4heSUMTm2CNTJFjt9AUDfaaZUZvdoh1QGhedXWkk/edit?usp=sharing ).

Passing to QA. Again, please test with this version of schema.xml (or newer) in place: https://github.com/IQSS/dataverse/blob/2ce1c4f7876af206913df36f4703e38026cb7596/conf/solr/4.6.0/schema.xml

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Original Redmine Comment
Author Name: Kevin Condon (@kcondon)
Original Date: 2014-05-01T23:48:47Z


Tested on 5/1

(mostly) Everything works as described.

The contributor facets are in the list but could not test due to another bug about not enabling facets.

Saw a minor issue where Wavelength Min was not appearing on the search results card but max and central wavelength. Will speak with Phil.

http://dvn-build.hmdc.harvard.edu/dataverse.xhtml?id=41&q=Wavelength+Min

FITS fields are not being added to dataset metadata because field names changed: astrotype, astrofacility, astroinstrument.

Leonid is aware of this and will add it to his FITS indexing ticket.

@eaquigley eaquigley added this to the Dataverse 4.0: Beta 1 milestone Jul 9, 2014
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Original Redmine Comment
Author Name: Kevin Condon (@kcondon)
Original Date: 2014-05-06T23:16:51Z


Tested on 5/6

All things work with the exception of a solr exception on multiple instances of multi value date fields. Opened as a separate ticket.

Also, as mentioned, fits ingest will be tested separately when ready.

Closing ticket

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