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A JSON-based rest service to process unstructured clinical text through a smart natural language processing system.

License: Other

Java 0.06% JavaScript 0.01% TSQL 99.94%

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Question: Where to run custom dictionary creator tool after getting ctakes rest service up and running?

I am very new to Ctakes and Java. I created a brand new ubuntu 18.04 VM and was able to follow the instructions to get the Ctakes rest service up.

However, I am now trying to follow Matthew's video to add custom dictionary for ICD codes, but I am not exactly sure where to find the runDictionaryCreator.sh from. I see the file in .../ctakes-rest-service/ctakes-codebase-area/trunk/ctakes-distribution/src/main/bin, but running the script from here throws this error:

Error: Could not find or load main class org.apache.ctakes.gui.dictionary.DictionaryCreator
Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.gui.dictionary.DictionaryCreator

Test with ctakes-friendly-web-ui

Sample web UI embedded in the REST module to test the same

When running in web server, does it use "resources" folder from "ctakes-rest-service/ctakes-web-rest/src/main/" or from the SVN branch we download it from?

Hello @MatthewVita @gandhirajan

Sorry to log it as an "issue"...... this is more of a question.

First of all, thank you for putting this together. It is so much helpful. I can get everything up and running with simple instructions listed on the intro page!

The reason I am asking above question is because I was looking at "Temporal module" and what it should give back and I saw some discrepancy.

Discrepancy I noticed is that I see TemporalSubPipe.piper file referencing "/org/apache/ctakes/temporal/ae/eventtime/model.jar" jar file. However, in "resources" folder in this Git repo, the path is actually "/org/apache/ctakes/temporal/ae/eventtime/20150629/model.jar"....notice the "20150629" date.

So, I wanted to know whether this is an issue or does Ctakes actually uses this model.jar from ctakes-temporal-res module >> resources folder?

If this is a stupid question, feel free to point it out :)

Thanks in advance for taking the time to answer to this question!!

JdbcRareWordDictionary Error

While running ctakes from web browser. The request gets process with 200 OK - POST.
The JSON returned is empty with following tomcat log error.

ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 INFO SentenceDetector - Starting processing.
17 Dec 2018 07:31:14 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.c takes.core.ae.TokenizerAnnotatorPTB
17 Dec 2018 07:31:14 INFO ContextDependentTokenizerAnnotator - process(JCas)
17 Dec 2018 07:31:14 INFO POSTagger - process(JCas)
17 Dec 2018 07:31:14 INFO Chunker - process(JCas)
17 Dec 2018 07:31:14 INFO ChunkAdjuster - process(JCas)
17 Dec 2018 07:31:14 INFO ChunkAdjuster - process(JCas)
17 Dec 2018 07:31:14 INFO AbstractJCasTermAnnotator - Finding Named Entities ...
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 ERROR JdbcRareWordDictionary - No operations allowed after statement closed.
17 Dec 2018 07:31:14 INFO AbstractJCasTermAnnotator - Finished processing
17 Dec 2018 07:31:14 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:http-nio-8080-exec-16

System Details and configs

UMLS tables;

PREFTERM
RXNORM
SNOMECT_US
TUI
cui_terms

Apache Tomcat : 8.0.23

lsb_release -a
LSB Version: core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch:core-4.1-amd64:core-4.1-noarch:cxx-3.0-amd64:cxx-3.0-noarch:cxx-3.1-amd64:cxx-3.1-noarch:cxx-3.2-amd64:cxx-3.2-noarch:cxx-4.0-amd64:cxx-4.0-noarch:cxx-4.1-amd64:cxx-4.1-noarch:security-4.0-amd64:security-4.0-noarch:security-4.1-amd64:security-4.1-noarch
Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty

Exception: The server time zone value X is unrecognized

If you get the following error:

java.sql.SQLException: The server time zone value 'X' is unrecognized or represents more than one time zone. You must configure either the server or JDBC driver (via the serverTimezone configuration property) to use a more specific time zone value if you want to utilize time zone support.

The solution is to run the following (in MySQL command line or other) with your specific timezone:

SET GLOBAL time_zone = '+5:30';
EXIT;

Limited Results with Various Inputs

Here are examples of inputs that return expected outputs when ran through the rest service:

the patient has hypertension
diabetes

Here is an example that returns nothing (from the cTAKES 4 User Guide ):

Dr. Nutritious Medical Nutrition Therapy for Hyperlipidemia Referral from: Julie Tester, RD, LD, CNSD Phone contact (and so on)........

...lastly, here are the QA results of me trying to get the correct results for the string string severe bipolar i disorder. It doesn't return anything as compared to a regular cTAKES run, which has the correct result.

I've been looking at this issue for a while. No success. Looking for help.

CTAKES Rest Service API throws error

Hi @gandhirajan ,

On using maven packaging with 'ctakes-rest-service' throws error..is there any documentation available

D:\cTakes\ctakes-rest-service-master\ctakes-rest-service>mvn package
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building ctakes-nlp-service 4.0.1
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for org.apache.ctakes:ctakes-type-system:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-core:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-core-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-dictionary-lookup:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-dictionary-lookup-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-dictionary-lookup-fast:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-dictionary-lookup-fast-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-preprocessor:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-pos-tagger:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-pos-tagger-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-chunker:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-chunker-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-lvg:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-lvg-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-context-tokenizer:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-clinical-pipeline:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-clinical-pipeline-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-ne-contexts:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-ne-contexts-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-assertion:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-assertion-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-assertion-zoner:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-assertion-zoner-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-constituency-parser:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-constituency-parser-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-coreference:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-coreference-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-drug-ner:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-drug-ner-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-side-effect:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-side-effect-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-smoking-status:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-smoking-status-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-dependency-parser:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-dependency-parser-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-relation-extractor-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-temporal:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.apache.ctakes:ctakes-temporal-res:jar:4.0.1-SNAPSHOT is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.146 s
[INFO] Finished at: 2017-12-06T12:51:00+05:30
[INFO] Final Memory: 7M/155M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project ctakes-nlp-service: Could not resolve dependencies for project org.apache.ctakes:ctakes-nlp-service:war:4.0.1: The following artifacts could not be resolved: org.apache.ctakes:ctakes-type-system:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-core:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-core-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-fast:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-fast-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-preprocessor:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-pos-tagger:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-pos-tagger-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-chunker:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-chunker-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-lvg:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-lvg-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-context-tokenizer:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-clinical-pipeline:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-clinical-pipeline-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ne-contexts:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ne-contexts-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion-zoner:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion-zoner-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-constituency-parser:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-constituency-parser-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-coreference:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-coreference-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-drug-ner:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-drug-ner-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-side-effect:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-side-effect-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-smoking-status:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-smoking-status-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dependency-parser:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dependency-parser-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-relation-extractor-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-temporal:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-temporal-res:jar:4.0.1-SNAPSHOT: Failure to find org.apache.ctakes:ctakes-type-system:jar:4.0.1-SNAPSHOT in file://D:\cTakes\ctakes-rest-service-master\ctakes-rest-service/repo was cached in the local repository, resolution will not be reattempted until the update interval of localrepository has elapsed or updates are forced -> [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/DependencyResolutionException

Better understand configuring optional tables in customDictionary.xml + write documentation

<!-- Optional tables for optional term info.
Uncommenting these lines alone may not persist term information;
persistence depends upon the TermConsumer.  -->
         <property key="rxnormTable" value="long"/>
         <property key="snomedct_usTable" value="long"/>
         <property key="mdrTable" value="long"/>

When the user builds their custom dictionary, we need to help them tell cTAKES that there are tables with this data. Perhaps the optional area of JdbcConceptFactory area is the best place?

Empty Annotations returned

I finally set up the API successfully. However, sending any text results in empty annotations. See screenshot attached:

I did try to set the umls credentials by editing the following two files:

ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper
ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper

However, it is not clear how we force ctakes to download whatever it needs from umls? Please advise... thanks!

Tomcat errors

On startup:

matthews-MacBook-Pro% catalina run
Using CATALINA_BASE:   /usr/local/Cellar/tomcat/9.0.4/libexec
Using CATALINA_HOME:   /usr/local/Cellar/tomcat/9.0.4/libexec
Using CATALINA_TMPDIR: /usr/local/Cellar/tomcat/9.0.4/libexec/temp
Using JRE_HOME:        /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home
Using CLASSPATH:       /usr/local/Cellar/tomcat/9.0.4/libexec/bin/bootstrap.jar:/usr/local/Cellar/tomcat/9.0.4/libexec/bin/tomcat-juli.jar
11-Feb-2018 18:53:34.049 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version:        Apache Tomcat/9.0.4
11-Feb-2018 18:53:34.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built:          Jan 18 2018 19:42:17 UTC
11-Feb-2018 18:53:34.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number:         9.0.4.0
11-Feb-2018 18:53:34.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name:               Mac OS X
11-Feb-2018 18:53:34.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version:            10.13.1
11-Feb-2018 18:53:34.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture:          x86_64
11-Feb-2018 18:53:34.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home:             /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre
11-Feb-2018 18:53:34.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version:           1.8.0_144-b01
11-Feb-2018 18:53:34.053 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor:            Oracle Corporation
11-Feb-2018 18:53:34.053 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE:         /usr/local/Cellar/tomcat/9.0.4/libexec
11-Feb-2018 18:53:34.053 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME:         /usr/local/Cellar/tomcat/9.0.4/libexec
11-Feb-2018 18:53:34.053 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/Cellar/tomcat/9.0.4/libexec/conf/logging.properties
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/Cellar/tomcat/9.0.4/libexec
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/Cellar/tomcat/9.0.4/libexec
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/Cellar/tomcat/9.0.4/libexec/temp
11-Feb-2018 18:53:34.054 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/Users/matthew/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:.]
11-Feb-2018 18:53:34.163 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
11-Feb-2018 18:53:34.181 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
11-Feb-2018 18:53:34.186 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
11-Feb-2018 18:53:34.187 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
11-Feb-2018 18:53:34.188 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 466 ms
11-Feb-2018 18:53:34.209 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
11-Feb-2018 18:53:34.209 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/9.0.4
11-Feb-2018 18:53:34.226 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/usr/local/Cellar/tomcat/9.0.4/libexec/webapps/ctakes-web-rest.war]
11-Feb-2018 18:53:38.382 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is  [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is  [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
11 Feb 2018 18:53:38  INFO DispatcherServlet - FrameworkServlet 'ctakes-rest-service': initialization started
11 Feb 2018 18:53:38  INFO XmlWebApplicationContext - Refreshing WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sun Feb 11 18:53:38 PST 2018]; root of context hierarchy
11 Feb 2018 18:53:38  INFO XmlBeanDefinitionReader - Loading XML bean definitions from ServletContext resource [/WEB-INF/ctakes-rest-service-servlet.xml]
11 Feb 2018 18:53:39  INFO RequestMappingHandlerMapping - Mapped "{[/analyze],methods=[POST]}" onto public java.util.Map<java.lang.String, java.util.Map<java.lang.String, java.util.List<java.lang.String>>> org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(java.lang.String,java.lang.String) throws java.lang.Exception
11 Feb 2018 18:53:39  INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sun Feb 11 18:53:38 PST 2018]; root of context hierarchy
11 Feb 2018 18:53:39  INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sun Feb 11 18:53:38 PST 2018]; root of context hierarchy
11 Feb 2018 18:53:39  INFO CtakesRestController - Initializing analysis engines and jcas pools
11 Feb 2018 18:53:39 ERROR PiperFileReader - Unknown Piper Command: threads
11 Feb 2018 18:53:39 ERROR PiperFileReader - Piper File not found: pipers/TsDefaultTokenizerPipeline
11 Feb 2018 18:53:40 ERROR PiperFileReader - Piper File not found: pipers/TsChunkerSubPipe
11 Feb 2018 18:53:40 ERROR PiperFileReader - Piper File not found: pipers/TsDictionarySubPipe
11 Feb 2018 18:53:40 ERROR PiperFileReader - Piper File not found: pipers/TsAttributeCleartkSubPipe
11 Feb 2018 18:53:40  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
11 Feb 2018 18:53:40  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
11 Feb 2018 18:53:43  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
11 Feb 2018 18:53:43  WARN PropertyAeFactory - No parameters specified.
11 Feb 2018 18:53:43  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
11 Feb 2018 18:53:43  WARN PropertyAeFactory - No parameters specified.
11 Feb 2018 18:53:43  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
11 Feb 2018 18:53:43  WARN PropertyAeFactory - No parameters specified.
11 Feb 2018 18:53:45 ERROR CtakesRestController - Error loading pipers
11 Feb 2018 18:53:45  WARN XmlWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
11 Feb 2018 18:53:45 ERROR DispatcherServlet - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
	at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
	at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
	at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
	at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
	at javax.servlet.GenericServlet.init(GenericServlet.java:158)
	at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1174)
	at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1090)
	at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:980)
	at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4829)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5139)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:740)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:716)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:703)
	at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:976)
	at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1847)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
	at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
	at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:761)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:431)
	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1575)
	at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:308)
	at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
	at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:424)
	at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:367)
	at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:964)
	at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:839)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
	at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1425)
	at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1415)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
	at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
	at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:941)
	at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:258)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
	at org.apache.catalina.core.StandardService.startInternal(StandardService.java:422)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
	at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:770)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
	at org.apache.catalina.startup.Catalina.start(Catalina.java:671)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:353)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:493)
Caused by: javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:98)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:85)
	at org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:60)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
	... 62 more
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.apache.ctakes.core.pipeline.PiperFileReader.getComponentClass(PiperFileReader.java:285)
	at org.apache.ctakes.core.pipeline.PiperFileReader.addToPipeline(PiperFileReader.java:217)
	at org.apache.ctakes.core.pipeline.PiperFileReader.parsePipelineLine(PiperFileReader.java:164)
	at org.apache.ctakes.core.pipeline.PiperFileReader.loadPipelineFile(PiperFileReader.java:146)
	at org.apache.ctakes.core.pipeline.PiperFileReader.<init>(PiperFileReader.java:114)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
	... 71 more
11-Feb-2018 18:53:45.325 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/Cellar/tomcat/9.0.4/libexec/webapps/ctakes-web-rest.war] has finished in [11,099] ms
11-Feb-2018 18:53:45.327 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
11-Feb-2018 18:53:45.332 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["ajp-nio-8009"]
11-Feb-2018 18:53:45.333 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 11144 ms

On POST:

11 Feb 2018 18:55:47  INFO DispatcherServlet - FrameworkServlet 'ctakes-rest-service': initialization started
11 Feb 2018 18:55:47  INFO XmlWebApplicationContext - Refreshing WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sun Feb 11 18:55:47 PST 2018]; root of context hierarchy
11 Feb 2018 18:55:47  INFO XmlBeanDefinitionReader - Loading XML bean definitions from ServletContext resource [/WEB-INF/ctakes-rest-service-servlet.xml]
11 Feb 2018 18:55:47  INFO RequestMappingHandlerMapping - Mapped "{[/analyze],methods=[POST]}" onto public java.util.Map<java.lang.String, java.util.Map<java.lang.String, java.util.List<java.lang.String>>> org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(java.lang.String,java.lang.String) throws java.lang.Exception
11 Feb 2018 18:55:47  INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sun Feb 11 18:55:47 PST 2018]; root of context hierarchy
11 Feb 2018 18:55:47  INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sun Feb 11 18:55:47 PST 2018]; root of context hierarchy
11 Feb 2018 18:55:47  INFO CtakesRestController - Initializing analysis engines and jcas pools
11 Feb 2018 18:55:47 ERROR PiperFileReader - Unknown Piper Command: threads
11 Feb 2018 18:55:47 ERROR PiperFileReader - Piper File not found: pipers/TsDefaultTokenizerPipeline
11 Feb 2018 18:55:48 ERROR PiperFileReader - Piper File not found: pipers/TsChunkerSubPipe
11 Feb 2018 18:55:48 ERROR PiperFileReader - Piper File not found: pipers/TsDictionarySubPipe
11 Feb 2018 18:55:48 ERROR PiperFileReader - Piper File not found: pipers/TsAttributeCleartkSubPipe
11 Feb 2018 18:55:48  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
11 Feb 2018 18:55:48  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
11 Feb 2018 18:55:49  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
11 Feb 2018 18:55:49  WARN PropertyAeFactory - No parameters specified.
11 Feb 2018 18:55:49  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
11 Feb 2018 18:55:49  WARN PropertyAeFactory - No parameters specified.
11 Feb 2018 18:55:49  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
11 Feb 2018 18:55:49  WARN PropertyAeFactory - No parameters specified.
11 Feb 2018 18:55:52 ERROR CtakesRestController - Error loading pipers
11 Feb 2018 18:55:52  WARN XmlWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
11 Feb 2018 18:55:52 ERROR DispatcherServlet - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
	at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
	at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
	at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
	at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
	at javax.servlet.GenericServlet.init(GenericServlet.java:158)
	at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1174)
	at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1090)
	at org.apache.catalina.core.StandardWrapper.allocate(StandardWrapper.java:770)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:133)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:651)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
	at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:417)
	at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
	at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:754)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1376)
	at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:748)
Caused by: javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:98)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:85)
	at org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:60)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
	... 38 more
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.apache.ctakes.core.pipeline.PiperFileReader.getComponentClass(PiperFileReader.java:285)
	at org.apache.ctakes.core.pipeline.PiperFileReader.addToPipeline(PiperFileReader.java:217)
	at org.apache.ctakes.core.pipeline.PiperFileReader.parsePipelineLine(PiperFileReader.java:164)
	at org.apache.ctakes.core.pipeline.PiperFileReader.loadPipelineFile(PiperFileReader.java:146)
	at org.apache.ctakes.core.pipeline.PiperFileReader.<init>(PiperFileReader.java:114)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
	... 47 more

Dosage strength is not returned in the response

Hello,

While trying to get the structured clinical data from the text, we have noticed that the drug strength is not parsed by the ctakes. I see that there is the component in the codebase "ctakes-drug-ner".

Is this component enabled by default? or do we have to enable it manually.

Here is the sample snapshot for same text from the CLAMP and CTAKES-REST-SERVICE:
CLAMP

ctakes-response:
{ "AnatomicalSiteMention": [ { "begin": 93, "end": 98, "text": "brain", "polarity": 1, "conceptAttributes": [ { "code": "12738006", "cui": "C0006104", "codingScheme": "SNOMEDCT_US", "tui": "T023" } ] }, { "begin": 160, "end": 164, "text": "hand", "polarity": 1, "conceptAttributes": [ { "code": "85562004", "cui": "C0018563", "codingScheme": "SNOMEDCT_US", "tui": "T023" } ] }, { "begin": 571, "end": 574, "text": "log", "polarity": 1, "conceptAttributes": [ { "code": "22735005", "cui": "C0228228", "codingScheme": "SNOMEDCT_US", "tui": "T023" } ] } ], "MedicationMention": [ { "begin": 175, "end": 180, "text": "today", "polarity": 1, "conceptAttributes": [ { "code": null, "cui": "C0310367", "codingScheme": "customDictionary", "tui": "T109" }, { "code": null, "cui": "C0310367", "codingScheme": "customDictionary", "tui": "T195" } ] }, { "begin": 218, "end": 225, "text": "namenda", "polarity": 1, "conceptAttributes": [ { "code": "405206", "cui": "C1330412", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "405206", "cui": "C1330412", "codingScheme": "RXNORM", "tui": "T109" } ] }, { "begin": 349, "end": 359, "text": "citalopram", "polarity": 1, "conceptAttributes": [ { "code": "321986007", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T109" }, { "code": "2556", "cui": "C0008845", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "2556", "cui": "C0008845", "codingScheme": "RXNORM", "tui": "T109" }, { "code": "372596005", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T121" }, { "code": "372596005", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T109" }, { "code": "321986007", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T121" } ] }, { "begin": 482, "end": 487, "text": "lasix", "polarity": 1, "conceptAttributes": [ { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T109" } ] }, { "begin": 597, "end": 602, "text": "lasix", "polarity": 1, "conceptAttributes": [ { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T109" } ] } ], "DrugChangeStatusAnnotation": [], "StrengthAnnotation": [], "FractionStrengthAnnotation": [], "FrequencyUnitAnnotation": [], "DiseaseDisorderMention": [ { "begin": 3, "end": 23, "text": "Alzheimer's dementia", "polarity": 1, "conceptAttributes": [ { "code": "26929004", "cui": "C0002395", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 15, "end": 23, "text": "dementia", "polarity": 1, "conceptAttributes": [ { "code": "52448006", "cui": "C0497327", "codingScheme": "SNOMEDCT_US", "tui": "T048" } ] }, { "begin": 366, "end": 385, "text": "Alzheimers dementia", "polarity": 1, "conceptAttributes": [ { "code": "26929004", "cui": "C0002395", "codingScheme": "SNOMEDCT_US", "tui": "T047" }, { "code": "142811000119104", "cui": "C3665464", "codingScheme": "SNOMEDCT_US", "tui": "T048" } ] }, { "begin": 377, "end": 385, "text": "dementia", "polarity": 1, "conceptAttributes": [ { "code": "52448006", "cui": "C0497327", "codingScheme": "SNOMEDCT_US", "tui": "T048" } ] }, { "begin": 467, "end": 470, "text": "CHF", "polarity": 1, "conceptAttributes": [ { "code": "42343007", "cui": "C0018802", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 934, "end": 943, "text": "infection", "polarity": 1, "conceptAttributes": [ { "code": "40733004", "cui": "C0009450", "codingScheme": "SNOMEDCT_US", "tui": "T047" }, { "code": "189822004", "cui": "C0009450", "codingScheme": "SNOMEDCT_US", "tui": "T047" }, { "code": "191415002", "cui": "C0009450", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 947, "end": 950, "text": "CHF", "polarity": 1, "conceptAttributes": [ { "code": "42343007", "cui": "C0018802", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 1073, "end": 1076, "text": "CHF", "polarity": 1, "conceptAttributes": [ { "code": "42343007", "cui": "C0018802", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] } ], "SignSymptomMention": [ { "begin": 228, "end": 232, "text": "mild", "polarity": 1, "conceptAttributes": [ { "code": "446411000124101", "cui": "C1513302", "codingScheme": "SNOMEDCT_US", "tui": "T033" } ] }, { "begin": 323, "end": 333, "text": "motivation", "polarity": 1, "conceptAttributes": [ { "code": "106121005", "cui": "C0026605", "codingScheme": "SNOMEDCT_US", "tui": "T041" }, { "code": "363882003", "cui": "C0026605", "codingScheme": "SNOMEDCT_US", "tui": "T041" } ] }, { "begin": 338, "end": 346, "text": "appetite", "polarity": 1, "conceptAttributes": [ { "code": "33911006", "cui": "C0003618", "codingScheme": "SNOMEDCT_US", "tui": "T040" } ] }, { "begin": 904, "end": 910, "text": "likely", "polarity": 1, "conceptAttributes": [ { "code": "2931005", "cui": "C0332148", "codingScheme": "SNOMEDCT_US", "tui": "T033" } ] }, { "begin": 911, "end": 925, "text": "cause of death", "polarity": 1, "conceptAttributes": [ { "code": "16100001", "cui": "C0007465", "codingScheme": "SNOMEDCT_US", "tui": "T033" }, { "code": "184305005", "cui": "C0007465", "codingScheme": "SNOMEDCT_US", "tui": "T033" } ] }, { "begin": 920, "end": 925, "text": "death", "polarity": 1, "conceptAttributes": [ { "code": "419620001", "cui": "C0011065", "codingScheme": "SNOMEDCT_US", "tui": "T040" } ] } ], "DateAnnotation": [ { "begin": 45, "end": 57, "text": "Apr 11, 2018", "polarity": 0, "conceptAttributes": [] }, { "begin": 67, "end": 79, "text": "Nov 04, 2015", "polarity": 0, "conceptAttributes": [] } ], "RouteAnnotation": [], "MeasurementAnnotation": [ { "begin": 255, "end": 260, "text": "23 mg", "polarity": 0, "conceptAttributes": [] }, { "begin": 621, "end": 626, "text": "2 lbs", "polarity": 0, "conceptAttributes": [] } ], "ProcedureMention": [ { "begin": 45, "end": 48, "text": "Apr", "polarity": 1, "conceptAttributes": [ { "code": "265414003", "cui": "C2004459", "codingScheme": "SNOMEDCT_US", "tui": "T061" } ] }, { "begin": 58, "end": 62, "text": "MMSE", "polarity": 1, "conceptAttributes": [ { "code": "273617000", "cui": "C0451306", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 80, "end": 84, "text": "MMSE", "polarity": 1, "conceptAttributes": [ { "code": "273617000", "cui": "C0451306", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 89, "end": 98, "text": "mri brain", "polarity": 1, "conceptAttributes": [ { "code": "29567006", "cui": "C0412675", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 89, "end": 92, "text": "mri", "polarity": 1, "conceptAttributes": [ { "code": "312250003", "cui": "C0024485", "codingScheme": "SNOMEDCT_US", "tui": "T060" }, { "code": "113091000", "cui": "C0024485", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 115, "end": 124, "text": "TREATMENT", "polarity": 1, "conceptAttributes": [ { "code": "277132007", "cui": "C0087111", "codingScheme": "SNOMEDCT_US", "tui": "T061" }, { "code": "276239002", "cui": "C0087111", "codingScheme": "SNOMEDCT_US", "tui": "T061" } ] }, { "begin": 564, "end": 570, "text": "weight", "polarity": 1, "conceptAttributes": [ { "code": "39857003", "cui": "C1305866", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 606, "end": 612, "text": "weight", "polarity": 1, "conceptAttributes": [ { "code": "39857003", "cui": "C1305866", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] } ], "TimeMention": [], "StrengthUnitAnnotation": [] }

StrengthAnnotation and FractionStrengthAnnotation are received empty.

Can you please point me in the right direction.

Thanks.

Perform custom dictionary testing

Next steps with the Spring Upgrade in place

@gandhirajan,

Thanks to your wonderful work on getting Spring updated in the core codebase, we can discuss what can be deleted from this codebase in terms of the copied Java files.

I am guessing we will be able to rid of the poms but may need to keep the code that alters the JDBC to work with MySQL? (I.E.: Switching out SimpleJdbcTemplate)

Thank you for being patient with me being on my trip. I realize I haven't been fast with my responses.

Could not resolve dependencies for project

I am following README of the project but getting below ERROR:

[ERROR] Failed to execute goal on project ctakes-distribution: Could not resolve dependencies for project org.apache.ctakes:ctakes-distribution:pom:4.0.1-SNAPSHOT: The following artifacts could not be resolved: org.apache.ctakes:ctakes-type-system:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-core:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-core-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-context-tokenizer:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-fast:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-fast-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-examples:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-examples-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-preprocessor:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-lvg:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-lvg-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-chunker:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-chunker-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ne-contexts:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ne-contexts-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-pos-tagger:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-pos-tagger-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dependency-parser:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dependency-parser-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-clinical-pipeline:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-clinical-pipeline-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-constituency-parser:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-constituency-parser-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-coreference:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-coreference-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-drug-ner:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-drug-ner-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-relation-extractor-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-side-effect:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-side-effect-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-smoking-status:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-smoking-status-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-temporal:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-temporal-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ytex:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ytex-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ytex-uima:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ytex-web:jar:classes:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-gui:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-gui-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-fhir:jar:4.0.1-SNAPSHOT: Could not transfer artifact org.apache.ctakes:ctakes-type-system:jar:4.0.1-20190719.123203-123 from/to apache.snapshots (http://repository.apache.org/snapshots): GET request of: org/apache/ctakes/ctakes-type-system/4.0.1-SNAPSHOT/ctakes-type-system-4.0.1-20190719.123203-123.jar from apache.snapshots failed: Premature end of Content-Length delimited message body (expected: 426524; received: 2375 -> [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/DependencyResolutionException

I am not that much familiar with how maven builds works internally. Thanks for any help.

TimeMention tag is not working

Temporal expression part is not working. I send an input as I had a back pain for four days ago which is not identified. It should identify this (for four days ago) word from the input

@MatthewVita Please check the issue as soon as possible.

FYI: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Temporal+Module

Use the current solutions as inspiration to finalize CtakesConceptMentionParser.java

Make CtakesHsqlToMysql.java parallel

Fix Dependency Security Issues

https://github.com/GoTeamEpsilon/ctakes-rest-service/network/alert/ctakes-web-rest/pom.xml/org.springframework:spring-core/closed

index.css:1 Failed to load resource: the server responded with a status of 404 ()

After a successful startup the api works for a single session only. On closing and restarting it the stops functioning and on looking for it's solution I found that the index.jsp has been given the reference of index.css from css directory which it is unable to find.
It's solution maybe to put the required file at it's place, but the file is not provided in the repository.
Please look into the issue.

Batch/Docker install script

Issue analyzing text after successful setup

Hey Matthew!

Thank you for updating the Readme instructions. It is clear and very very very helpful. I was able to follow the instructions and start the tomcat server successfully. However, when I try to analyze some text, I get below error:

22 Sep 2018 12:57:07  INFO DispatcherServlet - FrameworkServlet 'ctakes-rest-service': initialization started
22 Sep 2018 12:57:07  INFO XmlWebApplicationContext - Refreshing WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sat Sep 22 12:57:07 PDT 2018]; root of context hierarchy
22 Sep 2018 12:57:07  INFO XmlBeanDefinitionReader - Loading XML bean definitions from ServletContext resource [/WEB-INF/ctakes-rest-service-servlet.xml]
22 Sep 2018 12:57:07  INFO RequestMappingHandlerMapping - Mapped "{[/analyze],methods=[POST]}" onto public java.util.Map<java.lang.String, java.util.Map<java.lang.String, java.util.List<java.lang.String>>> org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(java.lang.String,java.util.Optional<java.lang.String>) throws java.lang.Exception
22 Sep 2018 12:57:07  INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sat Sep 22 12:57:07 PDT 2018]; root of context hierarchy
22 Sep 2018 12:57:07  INFO RequestMappingHandlerAdapter - Looking for @ControllerAdvice: WebApplicationContext for namespace 'ctakes-rest-service-servlet': startup date [Sat Sep 22 12:57:07 PDT 2018]; root of context hierarchy
22 Sep 2018 12:57:07  INFO CtakesRestController - Initializing analysis engines and jcas pools
22 Sep 2018 12:57:07 ERROR PiperFileReader - Unknown Piper Command: threads
22 Sep 2018 12:57:07 ERROR PiperFileReader - Piper File not found: pipers/TsDefaultTokenizerPipeline
22 Sep 2018 12:57:08 ERROR PiperFileReader - Piper File not found: pipers/TsChunkerSubPipe
22 Sep 2018 12:57:08 ERROR PiperFileReader - Piper File not found: pipers/TsDictionarySubPipe
22 Sep 2018 12:57:08 ERROR PiperFileReader - Piper File not found: pipers/TsAttributeCleartkSubPipe
22 Sep 2018 12:57:08  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
22 Sep 2018 12:57:08  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
22 Sep 2018 12:57:09  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
22 Sep 2018 12:57:09  WARN PropertyAeFactory - No parameters specified.
22 Sep 2018 12:57:09  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
22 Sep 2018 12:57:09  WARN PropertyAeFactory - No parameters specified.
22 Sep 2018 12:57:09  WARN PiperFileReader - Attempted to set Parameter by Command-line options.  Command-line options are not specified.
22 Sep 2018 12:57:09  WARN PropertyAeFactory - No parameters specified.
22 Sep 2018 12:57:11 ERROR CtakesRestController - Error loading pipers
22 Sep 2018 12:57:11  WARN XmlWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
22 Sep 2018 12:57:11 ERROR DispatcherServlet - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
	at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
	at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
	at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
	at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
	at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
	at javax.servlet.GenericServlet.init(GenericServlet.java:158)
	at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1144)
	at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1091)
	at org.apache.catalina.core.StandardWrapper.allocate(StandardWrapper.java:773)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:133)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
	at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
	at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
	at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
	at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:745)
Caused by: javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:104)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
	at org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:63)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
	at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
	... 38 more
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for LabValueFinder
	at org.apache.ctakes.core.pipeline.PiperFileReader.getComponentClass(PiperFileReader.java:285)
	at org.apache.ctakes.core.pipeline.PiperFileReader.addToPipeline(PiperFileReader.java:217)
	at org.apache.ctakes.core.pipeline.PiperFileReader.parsePipelineLine(PiperFileReader.java:164)
	at org.apache.ctakes.core.pipeline.PiperFileReader.loadPipelineFile(PiperFileReader.java:146)
	at org.apache.ctakes.core.pipeline.PiperFileReader.<init>(PiperFileReader.java:114)
	at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:97)
	... 47 more

I think I followed all of the instructions correctly. But, if I missed it then please feel free to call it out.

Thanks!!

Maven Error

Getting an error on step 7 line 2 (mvn install -Dmaven.test.skip=true). Have included the logs below. Not a core Java/Maven user. Any help would be appreciated.

[INFO] Scanning for projects...
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES Distribution 4.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for org.glassfish:javax.el:jar:3.0.1-b06-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.glassfish:javax.el:jar:3.0.1-b07-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.glassfish:javax.el:jar:3.0.1-b08-SNAPSHOT is missing, no dependency information available
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-distribution ---
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 17.307 s
[INFO] Finished at: 2018-10-30T19:50:23+05:30
[INFO] Final Memory: 25M/230M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-remote-resources-plugin:1.4:process (default) on project ctakes-distribution: Error finding remote resources manifests: /home/subu/Downloads/ctakes-rest-service/ctakes-codebase-area/trunk/ctakes-distribution/target/maven-shared-archive-resources/META-INF/NOTICE (No such file or directory) -> [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/MojoExecutionException

Question: How to update snowmed database?

Service to use multiple pipeline types

Email from Sean F:

You could actually run 1 service with multiple available pipeline types.  In other words, instead of running one service with default clinical, one with temporal, one with coref ...  You could run one service and just feed it an extra post parameter to choose which pipeline to run.  By default it would be clinical.

What do you think?  Obviously we should just make sure that it is working as-is, but after that it is really easy to add the extra functionality.

You can actually read as many piper files as you want and create multiple pipelines from them.  There are now thread safe versions of the most common annotators.  These could be used to minimize memory requirements by preventing multiple copies of models and dictionaries.  The service should still be serial.

Basically, the code would be as follows:

Static private final class PipelineRunner {
        Private final AnalysisEngineDescription _engine;
        Private final JCasPool _pool;
        Private PipelineRunner( final String piperPath ) {
                PiperFileReader reader = new PiperFileReader( piperPath );
                PipelineBuilder builder = reader.getBuilder();
                AnalysisEngineDescription pipeline = builder. getAnalysisEngineDesc();
                _engine = UIMAFramework.produceAnalysisEngine( pipeline );
                _pool = new JCasPool( 10, _engine );
        }
        Public void process( final String text ) {
                JCas jcas = _pool.getJCas( -1 );
                jcas.setDocumentText( text );
                _engine.process( jcas );
                _pool.releaseJCas( jcas );
        }
}

Static private Final Map<String,PipelineRunner> _pipelineRunners = new HashMap<>();
_pipelineRunners.put( "Default", new PipelineRunner( "TsDefaultClinicalPiperPath" ) );
_pipelineRunners.put( "Relations", new PipelineRunner( "TsRelationPiperPath" ) );
_pipelineRunners.put( "Temporal", new PipelineRunner( "TsTemporalPiperPath" ) );
_pipelineRunners.put( "Coreference", new PipelineRunner( "TsCoreferencePiperPath" ) );
_pipelineRunners.put( "Full", new PipelineRunner( "TsFullPiperPath" ) );

For each post:
String pipelineName = request.getParameter( "pipeline" );
If (pipelineName == null ) {
        pipelineName = "default";
}
Final PipelineRunner runner = _pipelineRunners.get( pipelineName );
If ( runner == null ) {
        handleError();
}
Final String text = request.getParameter( "text" );
runner.run( text );


It should be that simple.  You could also swap the map with an enum and fetch by pipeline name, but I don't think that it would gain anything.

Work with Sean and Tim to do SVN merge

"Can't call commit when autocommit=true" error in MySQL dictionary builder

03 Feb 2018 22:51:34  INFO MrConsoParser - File Lines: 349343 Concepts: 79397  Texts: 131122
03 Feb 2018 22:51:34  INFO DictionaryBuilder - Performing Poor man's WSD ...
03 Feb 2018 22:51:35  INFO DictionaryBuilder - Concepts: 79397  Texts: 130997
03 Feb 2018 22:51:35  INFO DictionaryBuilder - Done Parsing Concepts
03 Feb 2018 22:51:35  INFO DictionaryBuilder - Selected dictionary destination MySQL
03 Feb 2018 22:51:35  INFO JdbcUtil - Connecting to jdbc:mysql://localhost:3306/umls as root
03 Feb 2018 22:51:35  INFO DictionaryBuilder - Creating MySQL connection
03 Feb 2018 22:51:35  INFO DictionaryBuilder - writing concepts...
03 Feb 2018 22:56:06  INFO RareWordDbWriter - Main Table Rows 100000
03 Feb 2018 22:57:35 ERROR RareWordDbWriter - Can't call commit when autocommit=true
03 Feb 2018 22:57:35 ERROR MainPanel - Dictionary custom could not be built in /Users/matthew/ctakes-rest-service/ctakes-codebase-area/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT

Setup complete but cannot get project running as per README

Hi Folks,

I'm super happy that this is an open source project and thank you so much for starting it!

However, Im stuck.
I've installed (no errors!) on a Ubuntu (Xenial) server in AWS however, we're at a loss regarding the next steps as the README is not clear yet.

We've the system up and running (docker-compose start) and can see that the webserver is listening on 8080 (verified by telnet)

Hoever, when we send a POST as per the documentation -- nothing happens.

Any help would be greatly appreciated as I'd love to get this up and running and contribute back to the project.

Thanks in advance!
JP

Write press release

Handle CORS in REST module

Handle Cross Origin Resource Sharing in REST module

If I just clone the ctakes-rest-service ignore the code-base-step

I mean if I just mvn install this project but ignore the svn project.
Ignore the following step ,what will happen ?

mkdir ctakes-codebase-area
cd ctakes-codebase-area
svn export 'https://svn.apache.org/repos/asf/ctakes/trunk'
cd trunk/ctakes-distribution
mvn install -Dmaven.test.skip=true
cd ../ctakes-assertion-zoner
mvn install -Dmaven.test.skip=true
cd ../../../ctakes-web-rest
mvn install

Setup docker-compose with a cTAKES container as well as a MySQL container

Inconsistent working of API

help needed ctakes-web-rest build failed

Hi All

i clone this repository and try to run this ctakes-web-rest.added the umls credential inside dictionary . try to build the maven package but it throws error.

[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.871 s
[INFO] Finished at: 2018-07-26T23:44:31+05:30
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project ctakes-web-rest: Could not resolve dependencies for project org.apache.ctakes:ctakes-web-rest:war:4.0.1: The following artifacts could not be resolved: org.apache.ctakes:ctakes-type-system:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-core:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-core-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-fast:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dictionary-lookup-fast-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-preprocessor:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-pos-tagger:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-pos-tagger-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-chunker:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-chunker-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-lvg:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-lvg-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-context-tokenizer:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-clinical-pipeline:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-clinical-pipeline-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ne-contexts:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-ne-contexts-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion-zoner:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-assertion-zoner-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-constituency-parser:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-constituency-parser-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-coreference:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-coreference-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-drug-ner:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-drug-ner-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-side-effect:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-side-effect-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-smoking-status:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-smoking-status-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dependency-parser:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-dependency-parser-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-relation-extractor-res:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-temporal:jar:4.0.1-SNAPSHOT, org.apache.ctakes:ctakes-temporal-res:jar:4.0.1-SNAPSHOT: Could not find artifact org.apache.ctakes:ctakes-type-system:jar:4.0.1-SNAPSHOT -> [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.

is there any other settings/configs needs to be done which i am missing.

Thanks
Swagat

Create a new ctakes module for rest service such that it gets built as part of ctakes main build

Does folder "sno_rx_16ab_db" contain all load scripts?

I successfully installed service. However, my MySQL loading was fast and I didn't get any meaningful results.

Setup basic auth in Spring Security

Question: Running Ctakes-rest-service on top of an existing ctakes user installation on windows

While I am able to follow the instructions and get the rest service up on a ubuntu server, I am lost as to how to make further customizations to the dictionary etc (due to the fact that maybe some steps are skipped when installing ctakes from source? I have trouble running the dictionarycreator tool as it complains about missing java classes. )

So my question is if its possible to use ctakes-rest-service on top of an existing ctakes 4.0.0 user installation which I have validated to be working correctly? Also is it possible to run ctakes-rest-service on a windows server?

Out of memory errors when querying API

I am not able to query the API after setting up. Specifically:

Querying http://localhost:8080/ctakes-web-rest/index.jsp returns valid HTML (I believe the index page). So the tomcat setup seems valid.

Issuing a POST to http://localhost:8080/ctakes-web-rest/service/analyze?pipeline=Default returns a 500 error. Investigating catalina.out shows a Java Heap OutOfMemory error, which seems strange since I am posting only a very small file (5 lines of medical jargon).

I am on an ubuntu 18 ec2 instance. Pretty beefy p2.xlarge (I believe it has 64GB RAM). Should not be running out of memory, so not sure what's going on. Any ideas?

Test with ctakes-friendly-web-viewer

Project Status?

What's the latest status on this project? I recently forked the repo and started working on dockerizing everything, but I have been running into quite a few issues that are pretty hard to pin down. Just want to check in since there hasn't been much activity recently and I want to make sure you guys are still planning on moving this code forward before I commit too much more time to it.

Fix/write unit tests

AWS Cloud Deployment

Figure out how to run with LetsEncrypt

ctakes-rest-service on Windows 10 - ERROR: Service 'ctakes_webserver' failed to build

First of all, I'd like to thank you for your work!

I try to run this ctakes-rest-service on my Windows 10 machine:

docker-compose up

Building ctakes_webserver
Step 1/5 : FROM tomcat:8.0
 ---> e0919ffed768
Step 2/5 : COPY . .
 ---> Using cache
 ---> af942ac032b3
Step 3/5 : ADD install.sh ./install.sh
 ---> Using cache
 ---> 3bfaf03514a2
Step 4/5 : RUN chmod +x ./install.sh
 ---> Using cache
 ---> 0f2ed44f0187
Step 5/5 : RUN ./install.sh
 ---> Running in e9bfb1368eac
/bin/sh: 1: ./install.sh: not found
ERROR: Service 'ctakes_webserver' failed to build: The command '/bin/sh -c ./install.sh' returned a non-zero code: 127

as you may see it is fail with the following:

ERROR: Service 'ctakes_webserver' failed to build: The command '/bin/sh -c ./install.sh' returned a non-zero code: 127

what I'm doing wrong and how to fix it ? Thanks !

Add MySQL toggle and functionality to Dictionary Creator GUI

Setup an env variable based secret that is sent with each request (precursor to Spring Security)

Another question

Hi @gandhirajan,

Just wanted to see if you were able to merge changes from Tim Miller in https://issues.apache.org/jira/browse/CTAKES-529?

Thanks!

Compilation error: ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java:[59,5] error: cannot find symbol

Occurs after calling: mvn install in ./ctakes-web-rest:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.4:compile (default-compile) on project ctakes-web-rest: Compilation failure: Compilation failure:
[ERROR] /home/michaeljtbrooks/Downloads/Installers/ctakes-rest-service-master/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java:[34,23] error: cannot find symbol
[ERROR] symbol: class PostConstruct
[ERROR] location: package javax.annotation
[ERROR] /home/michaeljtbrooks/Downloads/Installers/ctakes-rest-service-master/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java:[59,5] error: cannot find symbol
[ERROR] -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.4:compile (default-compile) on project ctakes-web-rest: Compilation failure
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:566)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
Caused by: org.apache.maven.plugin.CompilationFailureException: Compilation failure
at org.apache.maven.plugin.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:678)
at org.apache.maven.plugin.CompilerMojo.execute (CompilerMojo.java:128)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:566)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
[ERROR]
[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

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