I am working with UIMA-Alpha02 and am currently trying to build a jar to make a
standalone application. (not pear because we want our users to have just the
JDK and not require ecilpse or UIMA) In many cases we use maven to build and
package the jar and it runs fine. Other times the jar is broken so that the
pipeline will always fail with this stacktrace:
2017-08-17 14:53:54 [ERROR] DeidRunnerController.203: Throwing
java.lang.ExceptionInInitializerError: null
at
com.clinacuity.deid.ae.FileSystemCollectionReader.getNext(FileSystemCollectionReader.java:105)
~[deid-0.0.1-SNAPSHOT-jar-with-dependencies.jar:?]
at com.clinacuity.deid.ae.DeidPipeline.execute(DeidPipeline.java:109)
~[deid-0.0.1-SNAPSHOT-jar-with-dependencies.jar:?]
at
com.clinacuity.deid.gui.DeidPipelineTask.call(DeidPipelineTask.java:41)
~[deid-0.0.1-SNAPSHOT-jar-with-dependencies.jar:?]
at
com.clinacuity.deid.gui.DeidPipelineTask.call(DeidPipelineTask.java:9)
~[deid-0.0.1-SNAPSHOT-jar-with-dependencies.jar:?]
at javafx.concurrent.Task$TaskCallable.call(Task.java:1423)
~[jfxrt.jar:?]
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
~[?:1.8.0_121]
at java.lang.Thread.run(Thread.java:745) ~[?:1.8.0_121]
Caused by: org.apache.uima.cas.CASRuntimeException: A JCas class field
"documentType" is being initialized by non-framework (user) code before Type
System Commit for a type system with a corresponding type. Either change the
user load code to not do initialize, or to defer it until after the type system
commit.
at
org.apache.uima.cas.impl.TypeSystemImpl.getAdjustedFeatureOffset(TypeSystemImpl.java:2564)
~[deid-0.0.1-SNAPSHOT-jar-with-dependencies.jar:?]
at
com.clinacuity.deid.annotations.DocumentInformationAnnotation.<clinit>(DocumentInformationAnnotation.java:23)
~[deid-0.0.1-SNAPSHOT-jar-with-dependencies.jar:?]
... 7 more
I logged the JCas type system before this error occurs with this command:
jCas.getTypeSystem(), when it *passes* it shows the type system as this:
TypeSystem: Type System <2,016,464,189>:
uima.cas.TOP: super: <null>
uima.cas.Integer: super: uima.cas.TOP
uima.cas.Float: super: uima.cas.TOP
uima.cas.String: super: uima.cas.TOP
uima.cas.ArrayBase: super: uima.cas.TOP
uima.cas.ListBase: super: uima.cas.TOP
uima.cas.Boolean: super: uima.cas.TOP
uima.cas.Byte: super: uima.cas.TOP
uima.cas.Short: super: uima.cas.TOP
uima.cas.Long: super: uima.cas.TOP
uima.cas.Double: super: uima.cas.TOP
uima.cas.Sofa: super: uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
sofaNum/uima.cas.Integer/F,
sofaID/uima.cas.String/F,
mimeType/uima.cas.String/F,
sofaArray/uima.cas.TOP/T,
sofaString/uima.cas.String/F,
sofaURI/uima.cas.String/F]
uima.cas.AnnotationBase: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
sofa/uima.cas.Sofa/F]
com.clinacuity.deid.uima.core.type.Lemma: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
key/uima.cas.String/F,
posTag/uima.cas.String/F]
com.clinacuity.deid.uima.core.type.OntologyConcept: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
codingScheme/uima.cas.String/F,
code/uima.cas.String/F,
oid/uima.cas.String/F]
but when it *fails* I get this:
TypeSystem: Type System <815,926,310>:
uima.cas.TOP: super: <null>
uima.cas.Integer: super: uima.cas.TOP
uima.cas.Float: super: uima.cas.TOP
uima.cas.String: super: uima.cas.TOP
uima.cas.ArrayBase: super: uima.cas.TOP
uima.cas.ListBase: super: uima.cas.TOP
uima.cas.Boolean: super: uima.cas.TOP
uima.cas.Byte: super: uima.cas.TOP
uima.cas.Short: super: uima.cas.TOP
uima.cas.Long: super: uima.cas.TOP
uima.cas.Double: super: uima.cas.TOP
uima.cas.Sofa: super: uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
sofaNum/uima.cas.Integer/F,
sofaID/uima.cas.String/F,
mimeType/uima.cas.String/F,
sofaArray/uima.cas.TOP/T,
sofaString/uima.cas.String/F,
sofaURI/uima.cas.String/F]
uima.cas.AnnotationBase: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
sofa/uima.cas.Sofa/F]
org.apache.ctakes.typesystem.type.refsem.Element: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
id/uima.cas.Integer/F,
ontologyConcept/org.apache.ctakes.typesystem.type.refsem.OntologyConcept/F,
mentions/org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation[]/F,
discoveryTechnique/uima.cas.Integer/F,
confidence/uima.cas.Double/F,
conditional/uima.cas.Boolean/F,
generic/uima.cas.Boolean/F,
subject/uima.cas.String/F,
polarity/uima.cas.Integer/F,
uncertainty/uima.cas.Integer/F,
historyOf/uima.cas.Integer/F]
org.apache.ctakes.typesystem.type.refsem.EventProperties: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
contextualModality/uima.cas.String/F,
contextualAspect/uima.cas.String/F,
permanence/uima.cas.String/F,
category/uima.cas.String/F,
aspect/uima.cas.String/F,
docTimeRel/uima.cas.String/F,
degree/uima.cas.String/F,
polarity/uima.cas.Integer/F]
org.apache.ctakes.typesystem.type.refsem.OntologyConcept: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
codingScheme/uima.cas.String/F,
code/uima.cas.String/F,
oid/uima.cas.String/F,
oui/uima.cas.String/F,
score/uima.cas.Double/F,
disambiguated/uima.cas.Boolean/F]
org.apache.ctakes.typesystem.type.relation.Relation: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
id/uima.cas.Integer/F,
category/uima.cas.String/F,
discoveryTechnique/uima.cas.Integer/F,
confidence/uima.cas.Double/F,
polarity/uima.cas.Integer/F,
uncertainty/uima.cas.Integer/F,
conditional/uima.cas.Boolean/F]
org.apache.ctakes.typesystem.type.relation.RelationArgument: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
id/uima.cas.Integer/F,
argument/uima.tcas.Annotation/F,
role/uima.cas.String/F,
participatesIn/uima.cas.FSList/F]
org.apache.ctakes.typesystem.type.structured.Demographics: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
birthDate/uima.cas.String/F,
deathDate/uima.cas.String/F,
gender/uima.cas.String/F,
firstName/uima.cas.String/F,
middleName/uima.cas.String/F,
lastName/uima.cas.String/F,
firstNameSoundex/uima.cas.String/F,
lastNameSoundex/uima.cas.String/F]
org.apache.ctakes.typesystem.type.structured.DocumentClassification: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
label/uima.cas.String/F]
org.apache.ctakes.typesystem.type.structured.DocumentID: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
documentID/uima.cas.String/F]
org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
documentIdPrefix/uima.cas.String/F]
org.apache.ctakes.typesystem.type.structured.DocumentPath: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
documentPath/uima.cas.String/F]
org.apache.ctakes.typesystem.type.structured.Metadata: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
patientID/uima.cas.Long/F,
providerID/uima.cas.LongArray/F,
sourceData/org.apache.ctakes.typesystem.type.structured.SourceData/F,
demographics/org.apache.ctakes.typesystem.type.structured.Demographics/F]
org.apache.ctakes.typesystem.type.structured.SourceData: super:
uima.cas.TOP, FeaturesIntroduced/Range/multiRef: [
noteTypeCode/uima.cas.String/F,
noteSubTypeCode/uima.cas.String/F,
authorSpecialty/uima.cas.String/F,
documentStandard/uima.cas.String/F,
sourceInstanceId/uima.cas.String/F,
sourceRevisionNbr/uima.cas.Integer/F,
sourceRevisionDate/uima.cas.String/F,
sourceOriginalDate/uima.cas.String/F,
sourceInstitution/uima.cas.String/F,
sourceEncounterId/uima.cas.String/F,
sourceApplication/uima.cas.String/F]
org.apache.ctakes.typesystem.type.syntax.Lemma: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
key/uima.cas.String/F,
posTag/uima.cas.String/F]
org.apache.ctakes.typesystem.type.util.Pair: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
attribute/uima.cas.String/F,
value/uima.cas.String/F]
org.apache.ctakes.typesystem.type.util.Pairs: super: uima.cas.TOP,
FeaturesIntroduced/Range/multiRef: [
pairs/org.apache.ctakes.typesystem.type.util.Pair[]/F]
Note that cTakes is an external library built on top of UIMA, we used the UIMA
3 migration tool to modify the type system of cTakes (with the <Optional> bug
fixed that was in UIMA 3 in the spring).
Is anyone familiar with any issues with UIMA 3, maven, or jars that would cause
a race condition that occurs only on build? I'm really scratching my head on
this one.
I can provide more code related to creating the TypeSystemDescription, the
FileSystemCollectionReader, and the DocumentInformationAnnotation if needed.
Thanks,
Andrew
