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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #471
Date Wed, 16 Apr 2014 00:36:06 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/471/changes>

Changes:

[dligach] Print a sentence and all gold relations that are annotated in it.

[tmill] Made parser use uimafit-style configuration parameters.

[tmill] Made BagOfCUIsGenerator to take command line args.

[tmill] CTAKES-82: Added code to allow gcg trees to be used in TK feature extractors.

[tmill] CTAKES-82: A variety of high-level syntactic and semantic features.

[tmill] CTAKES-82: Print out additional context for temporal relation viewer.

[tmill] CTAKES-82: Changes to time normalization grammar to allow ordinal numbers.

[tmill] CTAKES-82: Event eval now works for i2b2, can now output i2b2-style xml for tlinks
and events.

[tmill] CTAKES-82: Bugfix -- i2b2 tlinks weren't being added to cas.

[tmill] CTAKES-82: Modify meta time expression extractor to read i2b2 data.

[tmill] CTAKES-82: Added option for writing output to i2b2 xml format.

[tmill] CTAKES-82: Clean-up of some code in the default temporal pipelines. Added simpler
preprocessor w/o umls stuff.

[tmill] CTAKES-82: Meta-time expression extractor fixed, made a separate class.

[tmill] CTAKES-82: Fixed a recnetly checked in error that broke anafora reading code in temporal.

[tmill] CTAKES-82: Code to read i2b2 xml and do evals on at least time spans.

[tmill] CTAKES-82: Fixed feature selection threshold to be logical and consistent across classes.

[tmill] CTAKES-82: Code cleanup in temporal project.

[dligach] added time unit - wise duration difference features

[stevenbethard] Adds trained EventAnnotator model and static createAnnotatorDescription()
method for it. No tests yet as it's unclear whether we want to load all the prerequisites
(e.g. UMLS) within a unit test. Also, all the other models are still missing.

[clin] For event-time relation evaluation: flip back the argument order for "OVERLAP" relations
if its order was flipped from the gold standard.

[dligach] Updates due to changes in time normalization logic

[dligach] moved duration-related stuff to duration package

[dligach] Moved some common code to Utils and modifed the logic a bit.

[dligach] added code needed to filter out d/d, s/s, drugs, procedures, general events that
have no duration data

[dligach] added a few more negation key words

[dligach] now outputting event duration distributions to a file

[dligach] minor fixes

[dligach] switch event duration extractor to using bethard timex normalizer

[dligach] refactoring related to new timex normalizer wrapper in Utils.

[dligach] Wrote a wrapper for Bethard normalizer that takes a timex string and returns a set
of time units

[dligach] Moved Utils class from .feature.duration to .duration package.

[dligach] deleted AEs used fro evaluating event durations from .ae package

[dligach] Moved a bunch of AEs used for evaluating duration features

[dligach] created new package for duration-related stuff

[chenpei] CTAKES-197 - Upgrade cTAKES to Java 7

[clin] add umls feature for DocTimeRel annotator

[dligach] added a quick wrapper for clearNLP lemmatizer

[seanfinan] No target in sight

[brittfitch] fix for infinite loop (follow on to ctakes-251)
code was expanding a span and trying to get the min start and erroneously setting start to
-1 if one of the potential starts was uninitialized.

[dligach] Feature extractor for time unit duration only

[dligach] moved mapping (bethard normalizer -> coarse time unit) to one place

[clin] Current DocTimeRel annotator with UMLS feature extractor.

[dligach] renamed to better reflect the purpose

[dligach] removed old/unused feature extractor

[clin] check in ContextualModality model file

[clin] check in DocTimeRel model file

[clin] comment out the tree kernel-based DocTimeRel annotator and evaluation code

[dligach] added removing leading '\n' char (e.g. event 'height' contains one for some reason)

[dligach] moved formatDistribution(...) to Utils since it's used by another class now

[dligach] now saving duration distributions in a file

[dligach] Added support for a new bin ("decade")

[james-masanz] CTAKES-290 swap usage of arg1 and arg2 from location of relation so bodyLocation
gets filled in correctly

[dligach] now keep track in a datastructure of time unit counts for all events in corpus

[dligach] added a method to map steven's fine-grained time units to more corase ones

[dligach] first version of class to extract event durations using CONTAINS relation

[james-masanz] more of fix for CTAKES-288 - index name change - creation of text relation
annotations has degree_of and location_of separated into two indexes, no longer just one with
BinaryTextRelation in the name

[james-masanz] more of fix for CTAKES-288 - separate out degree_of and location_of processing
into separate loops since separate fs indexes

[james-masanz] first part of fix for CTAKES-288

[dligach] AE to keep only those event-time relations where the event argument could be found
by ctakes dictionary lookup

[dligach] code to only preserve event-event relations that map to dictionary lookup-generated
events.

[dligach] added some comments

[clin] create tree-kernel-version DocTimeRel evaluation code, which will call DocTimeRelWithTreeAnnotator.
Tried to derived single constituent tree, and simple dependency tree.

[dligach] Code related to evaluating the effect of adding duration features for event-event
relations

[dligach] Moved pointer to duration distribution file to one place (Utils.java)

[dligach] Moved various utility methods used by duration-related classes to one place (feature.duration.Utils)

[tmill] Fix for feature extractor using umls features to look at events and entities.

[clin] temporal: for the event-time relation evaluation code, recursively delete temporal
folder

[dligach] refactored so that it can be now used for sign/symptoms as well as disease/disorders
(and other event mentions)

[swu] updated type system diagrams for new *TextRelation and *Modifier

[tmill] CTAKES-82: Add in list of feature configs and comment out cleartk-2.0-dependent code
to get to copmile hopefully.

[tmill] CTAKES-82: Major changes to assertion eval to make reading other corpora easier.

[tmill] Check in missing utility class from yesterday's checkins.

[tmill] CTAKES-94 and CTAKES-210: Fixe semantic classes to use InputStream and to read a file
instead of a directory.

[tmill] CTAKES-94: Fix to add semantics to dependency tree fragment representation.

[tmill] CTAKES-94: Refactored code for printing constituency/dependency representations for
training.

[tmill] CTAKES-94: Reads sharp seed/stratified, mipacq, i2b2 data, and has the train/test
splits for sharp data.

[tmill] Fix annotator to use input streams as in ctakes-210. Also checks in resource file
it uses.

[tmill] New code for reading fragment file as stream (ala CTAKES-210) and consistent cue word
file.

[tmill] Fixed to use InputStream instead of FileLocator as in ctakes-210.

[stevenbethard] Modifies temporal Evaluation_ImplBase so that the text directory does not
need to be specified when Anafora format is used. (The text will be taken from the Anafora
directories.)

[tmill] Removed some unused imports.

[tmill] REmoved unused import.

[tmill] CTAKES-82: Refactored pipelines, including new pipeline that runs event-time relation
annotator with placeholder for event-event relations.

[tmill] CTAKES-82: Refactored some small annotators into super class.

[tmill] CTAKES-82: Add null check for contextual modality in tree kernel features -- needed
for using system inputs.

[dligach] forgot to lowercase the timex(s) last time

[dligach] a script useful for checking which temporal expressions in gold data can be normalized
by steve bethard's normalizer

[clin] Enable event properties evaluation models to be trained on both training and developing
data, test on the testing data, with "--test" option.

[brittfitch] CTAKES-281
prevent SQLException on null row in external resource file.

[tmill] Added short names to options in temporal.

[tmill] CTAKES-280: Fixes option handling for temporal data analysis package.

[tmill] Removed redundant dpeendencies in temporal pom.

[tmill] Addresses CTAKES-258: Fixes options in ctakes-temporal pipelines.

[tmill] Addresses CTAKES-82: Implements cleartk baselines for relations.

[james-masanz] replaced with cTAKES_clinical_pipeline.groovy (using underscores in script
name instead of dashes so that you can define a function within the file - otherwise end up
with invalid class name)

[james-masanz] CTAKES-273 - when script sets up classpath, add ctakes-resources to classpath
before ctakes so the full, separately-downloadable resources are used such as for LVG rather
than the partial/small resources that are included within cTAKES.

[james-masanz] replace script that has dashes in name with underscores

[james-masanz] Add SRL and dep parser (remove TODOs).  Set TypePriorities to ensure don't
get odd inconsistent behaviors like java.lang.RuntimeException: First token in sentence not
found!! from CharacterOffsetToLineTokenConverterCtakesImpl.

[dligach] AE to remove all events from gold view except those that have duration data

[dligach] refactoring/removed unused imports

[dligach] refactoring

[dligach] added logic to remove events and times that have no duration data

[dligach] assume gold only has relations that have duration data

[dligach] now using difference in seconds between durations of time and event

[dligach] deleted old version

[dligach] fixed a bug; now checking for type of arg1/2

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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.syntax.UCP_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.syntax.VP'.
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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.syntax.WordToken'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.syntax.WordToken_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.BodySideModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.BodySideModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ConditionalModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ContextAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.CourseModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.CourseModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.DateAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.DateAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.EntityMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.EntityMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.EventMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.EventMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.FractionAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.FractionAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.GenericModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabValueModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.LabValueModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationEventMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type'.
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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier_Type'.
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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.Modifier'.
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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation_Type'.
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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type'.
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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.Predicate_Type'.
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[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.RangeAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SemanticArgument'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SeverityModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SignSymptomMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SubjectModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.TimeAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.TimeMention'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.TimeMention_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.List'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.List_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.Paragraph'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.Paragraph_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.Segment'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.Segment_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.Sentence'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.textspan.Sentence_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.util.Pair'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.util.Pair_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.util.Pairs'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.util.Pairs_Type'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.util.ProbabilityDistribution'.
[INFO] JCasGen: Creating: 'org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type'.
[INFO] 
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[INFO] Compiling 313 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-type-system/target/classes>
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] Failure executing javac, but could not parse the error:
javac: invalid target release: 1.7
Usage: javac <options> <source files>
use -help for a list of possible options

[INFO] 1 error
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Waiting for Jenkins to finish collecting data[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.4:compile
(default-compile) on project ctakes-type-system: Compilation failure
[ERROR] Failure executing javac, but could not parse the error:
[ERROR] javac: invalid target release: 1.7
[ERROR] Usage: javac <options> <source files>
[ERROR] use -help for a list of possible options
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following
articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :ctakes-type-system

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