Sorry Sebastien I still don't get what you are trying to do.
On Saturday, August 10, 2019, Sebastien Boussard <[email protected]> wrote:
> 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
> !!!"
>
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
