Hello Mr. Rajan,
I have realized that I have sent you no context! I am currently working on the
Process Lines Clinical Runner. Previously, I was having many errors with the
directories. I made a link from my resources folder to the apache takes
resources folder. I have no link between the source code and the user interface.
Here is the code:
import java.io.File;
import java.io.IOException;
import org.apache.ctakes.core.cr.LinesFromFileCollectionReader;
import org.apache.ctakes.core.pipeline.EntityCollector;
import org.apache.ctakes.core.pipeline.PipelineBuilder;
import org.apache.ctakes.core.pipeline.PiperFileReader;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator;
import org.apache.uima.UIMAException;
import org.apache.log4j.Logger;
final public class ClinicalProcessor {
static private final Logger LOGGER =
Logger.getLogger("ClinicalProcessor");
static private final String PIPER_FILE_PATH =
"/Users/sboussard/Desktop/apache-ctakes-4.0.0/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper";
static private final String INPUT_FILE_PATH =
"/Users/sboussard/Desktop/apache-ctakes-4.0.0/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy";
private ClinicalProcessor() {
}
public static void main( final String[] args ) {
System.out.println(PIPER_FILE_PATH);
try {
// Create a piper file reader, but don't load the
piper yet - we want to create a reader with parameters
final PiperFileReader reader = new PiperFileReader();
final PipelineBuilder builder = reader.getBuilder();
// Add the Lines from File reader
//final File inputFile = FileLocator.locateFile(
INPUT_FILE_PATH );
//final File inputFile = FileLocator.getFile(
INPUT_FILE_PATH );
final File inputFile = new
File("/Users/sboussard/Desktop/ClampMac_1.6.0/workspace/MyPipeline/clamp-ner/Data/Input/sample_2788.txt");
builder.reader( LinesFromFileCollectionReader.class,
LinesFromFileCollectionReader.PARAM_INPUT_FILE_NAME,
inputFile.getAbsolutePath() );
// Add the lines from the piper file
reader.loadPipelineFile( PIPER_FILE_PATH );
// Collect IdentifiedAnnotation object information for
output - simple for examples
builder.collectEntities();
// Run the pipeline with specified text
builder.run();
// Log the IdentifiedAnnotation object information
LOGGER.info( "\n" +
EntityCollector.getInstance().toString() );
} catch ( IOException | UIMAException multE ) {
LOGGER.error( multE.getMessage() );
}
}
}
Thank you for all your help,
Sebastien Boussard
> On Aug 10, 2019, at 3:00 AM, gandhi rajan <[email protected]> wrote:
>
> As far as I know, it's a more generic error. Could you please let us know
> what action you are trying to perform and steps involved in reproducing the
> issue.
>
> On Saturday, August 10, 2019, Sebastien Boussard <[email protected]> wrote:
>
>> Hello,
>> I’m an intern in the Stanford Biomedical Informatics Lab and I've been
>> working on getting a ctakes page for a week, and I’ve been getting a lot of
>> errors. I have been getting a filed to initialize error for the last day
>> and a half and I can not solve it. I will send you the whole log, if you
>> can help me out it would be greatly appreciated.
>>
>> 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].
>> /Users/sboussard/Desktop/apache-ctakes-4.0.0/resources/
>> org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
>> 09 Aug 2019 11:28:50 INFO SentenceDetector - Sentence detector model
>> file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
>> 09 Aug 2019 11:28:50 INFO TokenizerAnnotatorPTB - Initializing
>> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
>> 09 Aug 2019 11:28:50 INFO ContextDependentTokenizerAnnotator - Finite
>> state machines loaded.
>> 09 Aug 2019 11:28:50 INFO POSTagger - POS tagger model file:
>> org/apache/ctakes/postagger/models/mayo-pos.zip
>> 09 Aug 2019 11:28:51 INFO Chunker - Chunker model file:
>> org/apache/ctakes/chunker/models/chunker-model.zip
>> 09 Aug 2019 11:28:52 INFO AbstractJCasTermAnnotator - Using dictionary
>> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
>> 09 Aug 2019 11:28:52 INFO AbstractJCasTermAnnotator - Exclusion tagset
>> loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN
>> VBP VBZ WDT WP WPS WRB
>> 09 Aug 2019 11:28:52 INFO AbstractJCasTermAnnotator - Using minimum term
>> text span: 3
>> 09 Aug 2019 11:28:52 INFO AbstractJCasTermAnnotator - Using Dictionary
>> Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
>> 09 Aug 2019 11:28:52 INFO DictionaryDescriptorParser - Parsing dictionary
>> specifications:
>> 09 Aug 2019 11:28:52 INFO UmlsUserApprover - Checking UMLS Account at
>> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard:
>> ..09 Aug 2019 11:28:53 INFO UmlsUserApprover - UMLS Account at
>> https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user boussard has
>> been validated
>>
>> 09 Aug 2019 11:28:53 ERROR ClinicalProcessor - Initialization of annotator
>> class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
>> failed. (Descriptor: <unknown>)
>>
>>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others !!!"
